Starting phenix.real_space_refine on Sat Apr 13 06:32:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byq_16331/04_2024/8byq_16331_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byq_16331/04_2024/8byq_16331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byq_16331/04_2024/8byq_16331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byq_16331/04_2024/8byq_16331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byq_16331/04_2024/8byq_16331_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byq_16331/04_2024/8byq_16331_neut_updated.pdb" } resolution = 4.1 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 16 6.06 5 P 394 5.49 5 Mg 1 5.21 5 S 435 5.16 5 C 53143 2.51 5 N 15215 2.21 5 O 16763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 85971 Number of models: 1 Model: "" Number of chains: 52 Chain: "0" Number of atoms: 5189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5189 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 25, 'TRANS': 627} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'GLU:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "1" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6034 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 727} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "2" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 2643 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 15, 'TRANS': 392} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 9 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 799 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 330 Chain: "3" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3589 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 429} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "4" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2710 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 347} Unresolved chain links: 1 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "5" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2064 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 253} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "7" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2233 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2370 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 279} 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: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 4051 Classifications: {'DNA': 198} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 197} 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: 4061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 4061 Classifications: {'DNA': 198} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 197} 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: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} 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: "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: 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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 6719 SG CYS 1 190 189.040 75.982 184.499 1.00226.10 S ATOM 6121 SG CYS 1 116 184.881 81.659 184.215 1.00219.17 S ATOM 6261 SG CYS 1 134 185.486 77.862 179.850 1.00290.04 S ATOM 6430 SG CYS 1 155 190.373 79.417 182.385 1.00254.08 S ATOM 19843 SG CYS 4 345 139.273 83.430 252.983 1.00519.14 S ATOM 19963 SG CYS 4 360 151.667 83.039 251.534 1.00419.38 S ATOM 19981 SG CYS 4 363 150.350 83.346 254.728 1.00448.30 S ATOM 20130 SG CYS 4 382 149.573 86.180 252.924 1.00439.17 S ATOM 20147 SG CYS 4 385 153.357 85.797 253.340 1.00448.60 S ATOM 19407 SG CYS 4 291 163.138 123.700 244.252 1.00342.35 S ATOM 19429 SG CYS 4 294 162.784 126.525 242.390 1.00352.59 S ATOM 19518 SG CYS 4 305 161.827 122.493 241.576 1.00358.38 S ATOM 19541 SG CYS 4 308 164.996 125.118 240.735 1.00333.33 S ATOM 22050 SG CYS 5 268 169.327 102.047 243.043 1.00345.39 S ATOM 22069 SG CYS 5 271 167.979 100.292 245.701 1.00354.72 S ATOM 22154 SG CYS 5 282 171.899 101.670 244.471 1.00324.81 S ATOM 22174 SG CYS 5 285 170.628 98.164 244.456 1.00314.19 S ATOM 22794 SG CYS 7 6 164.702 87.713 137.529 1.00384.92 S ATOM 22818 SG CYS 7 9 160.938 89.562 135.306 1.00391.12 S ATOM 22990 SG CYS 7 31 159.789 87.312 136.597 1.00354.97 S ATOM 22955 SG CYS 7 26 171.951 80.801 132.625 1.00306.02 S ATOM 23098 SG CYS 7 46 169.990 83.554 130.827 1.00366.96 S ATOM 23120 SG CYS 7 49 172.843 84.307 132.840 1.00358.01 S ATOM 30152 SG CYS A 71 142.992 100.028 94.964 1.00130.40 S ATOM 30174 SG CYS A 74 140.321 97.617 96.054 1.00119.91 S ATOM 30221 SG CYS A 81 139.488 100.959 94.506 1.00125.53 S ATOM 30456 SG CYS A 111 121.165 104.082 138.718 1.00256.86 S ATOM 30484 SG CYS A 114 122.345 100.804 139.281 1.00243.54 S ATOM 30797 SG CYS A 154 119.075 101.895 140.889 1.00200.60 S ATOM 30820 SG CYS A 184 122.473 103.377 142.205 1.00199.85 S ATOM 49607 SG CYS B1119 132.349 87.812 105.531 1.00141.85 S ATOM 49629 SG CYS B1122 131.683 91.347 107.015 1.00144.59 S ATOM 49744 SG CYS B1137 134.889 90.422 105.449 1.00136.41 S ATOM 49765 SG CYS B1140 134.033 88.878 108.763 1.00136.80 S ATOM 50745 SG CYS C 90 133.612 113.681 33.665 1.00123.28 S ATOM 50780 SG CYS C 94 134.066 115.963 31.435 1.00 97.69 S ATOM 50802 SG CYS C 97 130.882 115.890 33.763 1.00109.51 S ATOM 58088 SG CYS I 17 77.348 163.701 130.381 1.00219.05 S ATOM 58112 SG CYS I 20 80.868 162.332 129.597 1.00241.55 S ATOM 58273 SG CYS I 39 78.297 160.044 130.662 1.00251.56 S ATOM 58298 SG CYS I 42 79.763 162.964 133.057 1.00244.47 S ATOM 58650 SG CYS I 86 57.478 162.238 90.056 1.00173.28 S ATOM 58674 SG CYS I 89 58.010 165.483 87.966 1.00178.03 S ATOM 58878 SG CYS I 114 60.579 163.073 87.864 1.00207.98 S ATOM 58913 SG CYS I 119 59.793 165.043 91.120 1.00197.40 S ATOM 59024 SG CYS J 7 103.978 130.079 41.749 1.00 47.90 S ATOM 59048 SG CYS J 10 103.462 128.016 38.504 1.00 56.26 S ATOM 59312 SG CYS J 44 100.466 128.908 40.848 1.00 45.70 S ATOM 59318 SG CYS J 45 102.129 131.115 38.435 1.00 48.92 S ATOM 60438 SG CYS L 19 137.424 149.485 62.024 1.00 76.50 S ATOM 60457 SG CYS L 22 138.672 151.099 59.404 1.00 74.63 S ATOM 60574 SG CYS L 36 141.078 150.345 61.997 1.00 80.13 S ATOM 77916 SG CYS W 129 160.265 99.570 103.079 1.00629.93 S ATOM 77936 SG CYS W 132 157.051 101.416 103.781 1.00702.79 S ATOM 78108 SG CYS W 154 156.968 98.202 101.619 1.00431.09 S ATOM 78132 SG CYS W 157 158.285 101.436 100.329 1.00419.29 S Time building chain proxies: 32.40, per 1000 atoms: 0.38 Number of scatterers: 85971 At special positions: 0 Unit cell: (211.05, 216.3, 296.1, 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 16 29.99 Fe 4 26.01 S 435 16.00 P 394 15.00 Mg 1 11.99 O 16763 8.00 N 15215 7.00 C 53143 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: 29.96 Conformation dependent library (CDL) restraints added in 10.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 11000 " pdb="FE4 SF4 11000 " - pdb=" SG CYS 1 155 " pdb="FE1 SF4 11000 " - pdb=" SG CYS 1 190 " pdb="FE2 SF4 11000 " - pdb=" SG CYS 1 116 " 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 4 345 " pdb=" ZN 4 402 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 360 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 363 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 382 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 385 " pdb=" ZN 4 403 " pdb="ZN ZN 4 403 " - pdb=" SG CYS 4 291 " pdb="ZN ZN 4 403 " - pdb=" SG CYS 4 294 " pdb="ZN ZN 4 403 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 403 " - pdb=" SG CYS 4 305 " pdb=" ZN 5 401 " pdb="ZN ZN 5 401 " - pdb=" SG CYS 5 271 " pdb="ZN ZN 5 401 " - pdb=" SG CYS 5 282 " pdb="ZN ZN 5 401 " - pdb=" SG CYS 5 268 " pdb="ZN ZN 5 401 " - pdb=" SG CYS 5 285 " pdb=" ZN 7 400 " pdb="ZN ZN 7 400 " - pdb=" SG CYS 7 9 " pdb="ZN ZN 7 400 " - pdb=" SG CYS 7 31 " pdb="ZN ZN 7 400 " - pdb=" SG CYS 7 6 " pdb=" ZN 7 401 " pdb="ZN ZN 7 401 " - pdb=" ND1 HIS 7 28 " pdb="ZN ZN 7 401 " - pdb=" SG CYS 7 49 " pdb="ZN ZN 7 401 " - pdb=" SG CYS 7 46 " 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 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS 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 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " 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 45 " 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 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " 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 154 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " Number of angles added : 60 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18618 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 398 helices and 76 sheets defined 42.9% alpha, 11.1% beta 158 base pairs and 363 stacking pairs defined. Time for finding SS restraints: 29.94 Creating SS restraints... Processing helix chain '0' and resid 38 through 42 Processing helix chain '0' and resid 93 through 103 Processing helix chain '0' and resid 120 through 128 Processing helix chain '0' and resid 133 through 143 Processing helix chain '0' and resid 150 through 158 Processing helix chain '0' and resid 182 through 190 Processing helix chain '0' and resid 192 through 197 Processing helix chain '0' and resid 259 through 261 No H-bonds generated for 'chain '0' and resid 259 through 261' Processing helix chain '0' and resid 276 through 286 removed outlier: 3.895A pdb=" N LYS 0 282 " --> pdb=" O GLU 0 278 " (cutoff:3.500A) Processing helix chain '0' and resid 318 through 328 Processing helix chain '0' and resid 346 through 357 Processing helix chain '0' and resid 368 through 381 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: 3.846A pdb=" N GLU 0 428 " --> pdb=" O GLU 0 424 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP 0 429 " --> pdb=" O ARG 0 425 " (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 448 through 458 Processing helix chain '0' and resid 480 through 484 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 536 removed outlier: 3.638A pdb=" N TYR 0 534 " --> pdb=" O ILE 0 531 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET 0 536 " --> pdb=" O LEU 0 533 " (cutoff:3.500A) Processing helix chain '0' and resid 538 through 553 Processing helix chain '0' and resid 565 through 575 Processing helix chain '0' and resid 586 through 597 Processing helix chain '0' and resid 609 through 612 Processing helix chain '0' and resid 633 through 643 Processing helix chain '0' and resid 669 through 682 Processing helix chain '0' and resid 706 through 718 Processing helix chain '0' and resid 721 through 724 No H-bonds generated for 'chain '0' and resid 721 through 724' Processing helix chain '1' and resid 19 through 33 Processing helix chain '1' and resid 48 through 62 Processing helix chain '1' and resid 77 through 98 Processing helix chain '1' and resid 112 through 114 No H-bonds generated for 'chain '1' and resid 112 through 114' Processing helix chain '1' and resid 127 through 137 Processing helix chain '1' and resid 140 through 148 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 200 removed outlier: 4.271A pdb=" N LEU 1 200 " --> pdb=" O ARG 1 196 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 213 removed outlier: 3.549A pdb=" N LEU 1 213 " --> pdb=" O HIS 1 210 " (cutoff:3.500A) Processing helix chain '1' and resid 223 through 228 removed outlier: 4.278A pdb=" N LYS 1 228 " --> pdb=" O GLU 1 224 " (cutoff:3.500A) Processing helix chain '1' and resid 237 through 247 Processing helix chain '1' and resid 253 through 276 Processing helix chain '1' and resid 279 through 290 Processing helix chain '1' and resid 297 through 300 No H-bonds generated for 'chain '1' and resid 297 through 300' Processing helix chain '1' and resid 326 through 344 Processing helix chain '1' and resid 354 through 363 Processing helix chain '1' and resid 369 through 385 removed outlier: 5.032A pdb=" N ALA 1 376 " --> pdb=" O LEU 1 372 " (cutoff:3.500A) removed outlier: 5.170A 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 423 through 425 No H-bonds generated for 'chain '1' and resid 423 through 425' Processing helix chain '1' and resid 440 through 450 removed outlier: 3.916A pdb=" N LYS 1 445 " --> pdb=" O LEU 1 442 " (cutoff:3.500A) Proline residue: 1 446 - end of helix Processing helix chain '1' and resid 464 through 470 Proline residue: 1 468 - end of helix No H-bonds generated for 'chain '1' and resid 464 through 470' Processing helix chain '1' and resid 514 through 530 removed outlier: 3.518A pdb=" N ALA 1 529 " --> pdb=" O LEU 1 525 " (cutoff:3.500A) 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 587 Processing helix chain '1' and resid 603 through 607 removed outlier: 4.001A pdb=" N GLY 1 607 " --> pdb=" O VAL 1 604 " (cutoff:3.500A) Processing helix chain '1' and resid 630 through 643 Processing helix chain '1' and resid 648 through 667 removed outlier: 3.557A pdb=" N HIS 1 659 " --> pdb=" O ASP 1 655 " (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 698 No H-bonds generated for 'chain '1' and resid 695 through 698' Processing helix chain '1' and resid 703 through 705 No H-bonds generated for 'chain '1' and resid 703 through 705' Processing helix chain '1' and resid 710 through 724 Processing helix chain '1' and resid 732 through 734 No H-bonds generated for 'chain '1' and resid 732 through 734' Processing helix chain '1' and resid 741 through 745 Processing helix chain '1' and resid 747 through 756 removed outlier: 3.891A pdb=" N ARG 1 752 " --> pdb=" O THR 1 749 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE 1 753 " --> pdb=" O LEU 1 750 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU 1 754 " --> pdb=" O LYS 1 751 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN 1 755 " --> pdb=" O ARG 1 752 " (cutoff:3.500A) Processing helix chain '2' and resid 108 through 120 removed outlier: 4.159A pdb=" N GLU 2 112 " --> pdb=" O ASN 2 108 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU 2 113 " --> pdb=" O LYS 2 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN 2 115 " --> pdb=" O LEU 2 111 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ARG 2 116 " --> pdb=" O GLU 2 112 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N MET 2 117 " --> pdb=" O GLU 2 113 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU 2 118 " --> pdb=" O LYS 2 114 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 133 Processing helix chain '2' and resid 139 through 146 removed outlier: 4.222A pdb=" N TRP 2 143 " --> pdb=" O ALA 2 139 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ARG 2 146 " --> pdb=" O PHE 2 142 " (cutoff:3.500A) Processing helix chain '2' and resid 165 through 167 No H-bonds generated for 'chain '2' and resid 165 through 167' Processing helix chain '2' and resid 191 through 199 Processing helix chain '2' and resid 201 through 209 Processing helix chain '2' and resid 218 through 225 removed outlier: 4.481A pdb=" N PHE 2 225 " --> pdb=" O TRP 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 229 No H-bonds generated for 'chain '2' and resid 227 through 229' Processing helix chain '2' and resid 252 through 255 No H-bonds generated for 'chain '2' and resid 252 through 255' Processing helix chain '2' and resid 295 through 318 removed outlier: 3.801A pdb=" N GLY 2 318 " --> pdb=" O VAL 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 349 through 358 Processing helix chain '2' and resid 379 through 384 removed outlier: 3.660A pdb=" N HIS 2 384 " --> pdb=" O ARG 2 381 " (cutoff:3.500A) Processing helix chain '2' and resid 397 through 412 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 454 through 479 removed outlier: 3.702A pdb=" N HIS 2 463 " --> pdb=" O SER 2 459 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS 2 474 " --> pdb=" O GLU 2 470 " (cutoff:3.500A) Processing helix chain '2' and resid 486 through 514 removed outlier: 3.727A pdb=" N VAL 2 491 " --> pdb=" O GLU 2 487 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN 2 501 " --> pdb=" O LEU 2 497 " (cutoff:3.500A) Proline residue: 2 507 - end of helix removed outlier: 3.936A pdb=" N ILE 2 512 " --> pdb=" O PHE 2 508 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG 2 513 " --> pdb=" O GLN 2 509 " (cutoff:3.500A) Processing helix chain '2' and resid 523 through 541 removed outlier: 3.666A pdb=" N LEU 2 536 " --> pdb=" O ALA 2 532 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 25 removed outlier: 3.926A pdb=" N GLY 3 25 " --> pdb=" O GLU 3 21 " (cutoff:3.500A) Processing helix chain '3' and resid 28 through 36 Processing helix chain '3' and resid 38 through 47 Processing helix chain '3' and resid 50 through 59 Processing helix chain '3' and resid 68 through 74 Processing helix chain '3' and resid 77 through 92 removed outlier: 4.197A pdb=" N LYS 3 81 " --> pdb=" O LYS 3 77 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA 3 82 " --> pdb=" O GLU 3 78 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU 3 85 " --> pdb=" O LYS 3 81 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER 3 86 " --> pdb=" O ALA 3 82 " (cutoff:3.500A) Processing helix chain '3' and resid 112 through 122 Processing helix chain '3' and resid 145 through 164 Processing helix chain '3' and resid 173 through 181 Processing helix chain '3' and resid 190 through 192 No H-bonds generated for 'chain '3' and resid 190 through 192' Processing helix chain '3' and resid 198 through 205 Processing helix chain '3' and resid 208 through 223 Processing helix chain '3' and resid 230 through 241 Processing helix chain '3' and resid 256 through 267 Processing helix chain '3' and resid 285 through 288 No H-bonds generated for 'chain '3' and resid 285 through 288' Processing helix chain '3' and resid 322 through 331 removed outlier: 3.514A pdb=" N LEU 3 330 " --> pdb=" O ALA 3 326 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE 3 331 " --> pdb=" O LEU 3 327 " (cutoff:3.500A) Processing helix chain '3' and resid 348 through 356 Processing helix chain '3' and resid 361 through 370 Processing helix chain '3' and resid 374 through 376 No H-bonds generated for 'chain '3' and resid 374 through 376' Processing helix chain '3' and resid 385 through 398 removed outlier: 3.572A pdb=" N GLU 3 395 " --> pdb=" O ILE 3 391 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG 3 398 " --> pdb=" O TRP 3 394 " (cutoff:3.500A) Processing helix chain '3' and resid 415 through 428 Processing helix chain '3' and resid 445 through 456 removed outlier: 4.574A pdb=" N SER 3 449 " --> pdb=" O ALA 3 446 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL 3 451 " --> pdb=" O HIS 3 448 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG 3 453 " --> pdb=" O ASP 3 450 " (cutoff:3.500A) Processing helix chain '4' and resid 23 through 25 No H-bonds generated for 'chain '4' and resid 23 through 25' Processing helix chain '4' and resid 29 through 31 No H-bonds generated for 'chain '4' and resid 29 through 31' Processing helix chain '4' and resid 34 through 37 No H-bonds generated for 'chain '4' and resid 34 through 37' Processing helix chain '4' and resid 69 through 72 Processing helix chain '4' and resid 80 through 98 Processing helix chain '4' and resid 124 through 136 removed outlier: 4.470A pdb=" N ASP 4 136 " --> pdb=" O LYS 4 132 " (cutoff:3.500A) Processing helix chain '4' and resid 145 through 158 removed outlier: 4.416A pdb=" N HIS 4 158 " --> pdb=" O GLN 4 154 " (cutoff:3.500A) Processing helix chain '4' and resid 183 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 324 removed outlier: 3.531A pdb=" N ALA 4 319 " --> pdb=" O ALA 4 315 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER 4 321 " --> pdb=" O HIS 4 317 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS 4 323 " --> pdb=" O ALA 4 319 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS 4 324 " --> pdb=" O ARG 4 320 " (cutoff:3.500A) Processing helix chain '4' and resid 369 through 377 removed outlier: 3.677A pdb=" N HIS 4 376 " --> pdb=" O ASP 4 372 " (cutoff:3.500A) Processing helix chain '4' and resid 383 through 386 No H-bonds generated for 'chain '4' and resid 383 through 386' Processing helix chain '5' and resid 19 through 27 Processing helix chain '5' and resid 34 through 51 Processing helix chain '5' and resid 103 through 120 removed outlier: 3.584A pdb=" N ALA 5 107 " --> pdb=" O LEU 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 150 Processing helix chain '5' and resid 171 through 186 removed outlier: 4.901A pdb=" N MET 5 175 " --> pdb=" O LEU 5 172 " (cutoff:3.500A) Processing helix chain '5' and resid 201 through 210 Processing helix chain '5' and resid 220 through 230 removed outlier: 5.159A pdb=" N LEU 5 224 " --> pdb=" O PRO 5 221 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU 5 228 " --> pdb=" O GLN 5 225 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL 5 230 " --> pdb=" O LEU 5 227 " (cutoff:3.500A) Processing helix chain '5' and resid 235 through 238 No H-bonds generated for 'chain '5' and resid 235 through 238' Processing helix chain '6' and resid 14 through 25 Processing helix chain '6' and resid 47 through 65 removed outlier: 4.079A pdb=" N ASN 6 51 " --> pdb=" O ALA 6 47 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL 6 52 " --> pdb=" O GLU 6 48 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU 6 55 " --> pdb=" O ASN 6 51 " (cutoff:3.500A) Processing helix chain '7' and resid 11 through 15 Processing helix chain '7' and resid 32 through 40 Processing helix chain '7' and resid 66 through 81 removed outlier: 3.938A pdb=" N ILE 7 81 " --> pdb=" O LYS 7 77 " (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 111 Processing helix chain '7' and resid 114 through 127 Processing helix chain '7' and resid 134 through 189 Processing helix chain '7' and resid 194 through 209 removed outlier: 3.882A pdb=" N LEU 7 198 " --> pdb=" O VAL 7 194 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA 7 199 " --> pdb=" O ALA 7 195 " (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 275 removed outlier: 3.533A pdb=" N LEU 7 272 " --> pdb=" O LEU 7 269 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN 7 273 " --> pdb=" O GLY 7 270 " (cutoff:3.500A) Processing helix chain '7' and resid 280 through 284 Processing helix chain '7' and resid 289 through 301 removed outlier: 3.809A pdb=" N CYS 7 293 " --> pdb=" O SER 7 289 " (cutoff:3.500A) Processing helix chain '8' and resid 57 through 68 Processing helix chain '8' and resid 98 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: 3.560A pdb=" N MET 8 196 " --> pdb=" O GLY 8 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU 8 208 " --> pdb=" O GLU 8 205 " (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 275 Processing helix chain '8' and resid 286 through 290 Processing helix chain '8' and resid 293 through 296 No H-bonds generated for 'chain '8' and resid 293 through 296' 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 9 No H-bonds generated for 'chain '9' and resid 7 through 9' Processing helix chain '9' and resid 16 through 36 Processing helix chain '9' and resid 50 through 69 Processing helix chain '9' and resid 77 through 93 removed outlier: 4.355A pdb=" N ASN 9 93 " --> pdb=" O ARG 9 89 " (cutoff:3.500A) 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: 3.805A pdb=" N LEU 9 148 " --> pdb=" O LEU 9 144 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU 9 149 " --> pdb=" O GLU 9 145 " (cutoff:3.500A) Processing helix chain '9' and resid 163 through 177 removed outlier: 4.270A pdb=" N LYS 9 175 " --> pdb=" O LEU 9 171 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR 9 176 " --> pdb=" O ILE 9 172 " (cutoff:3.500A) Processing helix chain '9' and resid 184 through 200 removed outlier: 4.274A pdb=" N LYS 9 189 " --> pdb=" O ILE 9 186 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA 9 199 " --> pdb=" O ASN 9 196 " (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 260 removed outlier: 3.977A pdb=" N ARG 9 242 " --> pdb=" O LYS 9 239 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR 9 243 " --> pdb=" O GLU 9 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL 9 259 " --> pdb=" O ARG 9 256 " (cutoff:3.500A) Processing helix chain '9' and resid 267 through 282 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: 4.999A pdb=" N VAL A 101 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.983A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 4.111A 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 removed outlier: 3.500A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) No H-bonds generated for '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 566 removed outlier: 3.615A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 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: 3.746A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.018A 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 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 833 through 856 removed outlier: 3.585A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.571A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (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 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 994 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 Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.417A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1128 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'A' and resid 1151 through 1161 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 1187 through 1197 removed outlier: 4.002A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.898A 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: 7.559A pdb=" N ASP A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) removed outlier: 7.763A 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: 3.521A pdb=" N ILE A1288 " --> pdb=" O LEU A1285 " (cutoff:3.500A) removed outlier: 3.606A 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 Processing helix chain 'A' and resid 1395 through 1406 Processing helix chain 'A' and resid 1416 through 1421 removed outlier: 4.568A pdb=" N ARG A1421 " --> pdb=" O HIS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1435 through 1445 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: 4.294A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.598A 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 276 Processing helix chain 'B' and resid 281 through 288 removed outlier: 3.786A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 323 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 425 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 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' 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 539 through 547 removed outlier: 3.500A 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 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 4.004A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 4.372A 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: 3.958A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 741 removed outlier: 4.480A pdb=" N HIS B 741 " --> pdb=" O THR B 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 738 through 741' Processing helix chain 'B' and resid 762 through 767 Processing helix chain 'B' and resid 798 through 802 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: 3.660A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1057 No H-bonds generated for 'chain 'B' and resid 1055 through 1057' 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: 3.530A 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 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' 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: 3.558A 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 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 3 through 23 removed outlier: 4.184A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.594A 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: 3.844A 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 99 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 Processing helix chain 'I' and resid 64 through 67 No H-bonds generated for 'chain 'I' and resid 64 through 67' 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 38 Processing helix chain 'J' and resid 43 through 51 removed outlier: 3.618A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.797A 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 52 removed outlier: 3.937A 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 128 removed outlier: 3.689A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) 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: 3.518A pdb=" N PHE M 214 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET M 215 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER M 216 " --> pdb=" O ASP M 213 " (cutoff:3.500A) removed outlier: 3.709A 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: 4.696A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARG Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG Q 167 " --> pdb=" O GLU Q 163 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN Q 168 " --> pdb=" O TRP Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 179 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 123 through 136 Processing helix chain 'R' and resid 160 through 172 Processing helix chain 'R' and resid 180 through 193 removed outlier: 3.567A pdb=" N LYS R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 206 Processing helix chain 'R' and resid 210 through 220 removed outlier: 3.742A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 32 removed outlier: 4.414A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.446A 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 326 through 329 No H-bonds generated for 'chain 'U' and resid 326 through 329' Processing helix chain 'V' and resid 10 through 24 removed outlier: 3.524A pdb=" N LEU V 15 " --> pdb=" O LEU V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 51 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: 3.814A pdb=" N ASN W 142 " --> pdb=" O ASP W 138 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 194 removed outlier: 3.510A pdb=" N MET W 168 " --> pdb=" O GLU W 165 " (cutoff:3.500A) Proline residue: W 169 - end of helix removed outlier: 3.640A pdb=" N ASP W 172 " --> pdb=" O PRO W 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA W 173 " --> pdb=" O LYS W 170 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA W 178 " --> pdb=" O THR W 175 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE W 184 " --> pdb=" O ASN W 181 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU W 185 " --> pdb=" O GLU W 182 " (cutoff:3.500A) Proline residue: W 186 - end of helix Processing helix chain 'X' and resid 75 through 91 removed outlier: 3.528A pdb=" N GLN X 90 " --> pdb=" O LYS X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 105 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 179 through 188 removed outlier: 6.032A pdb=" N ASP X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLN X 188 " --> 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: 4.262A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 57 Processing helix chain 'a' and resid 65 through 79 removed outlier: 4.227A pdb=" N ASP a 78 " --> pdb=" O GLU a 74 " (cutoff:3.500A) removed outlier: 3.976A 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 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 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 22 Processing helix chain 'c' and resid 28 through 37 Processing helix chain 'c' and resid 46 through 73 removed outlier: 4.046A 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 94 through 97 No H-bonds generated for 'chain 'c' and resid 94 through 97' Processing helix chain 'c' and resid 114 through 116 No H-bonds generated for 'chain 'c' and resid 114 through 116' 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 Processing helix chain 'e' and resid 65 through 79 removed outlier: 3.623A pdb=" N PHE e 79 " --> pdb=" O ILE e 75 " (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 26 through 29 No H-bonds generated for 'chain 'f' and resid 26 through 29' 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: 4.019A 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: 5.784A pdb=" N LYS 0 117 " --> pdb=" O PRO 0 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 291 through 295 removed outlier: 7.392A pdb=" N VAL 0 166 " --> pdb=" O LEU 0 292 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N GLU 0 294 " --> pdb=" O VAL 0 166 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU 0 168 " --> pdb=" O GLU 0 294 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR 0 175 " --> pdb=" O VAL 0 272 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER 0 179 " --> pdb=" O VAL 0 268 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL 0 268 " --> pdb=" O SER 0 179 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 389 through 392 removed outlier: 6.039A pdb=" N VAL 0 405 " --> pdb=" O CYS 0 390 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE 0 392 " --> pdb=" O VAL 0 405 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE 0 407 " --> pdb=" O PHE 0 392 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS 0 361 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER 0 408 " --> pdb=" O CYS 0 361 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL 0 363 " --> pdb=" O SER 0 408 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU 0 437 " --> pdb=" O LEU 0 362 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU 0 364 " --> pdb=" O LEU 0 437 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE 0 439 " --> pdb=" O LEU 0 364 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY 0 336 " --> pdb=" O GLY 0 465 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR 0 467 " --> pdb=" O GLY 0 336 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE 0 338 " --> pdb=" O THR 0 467 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL 0 339 " --> pdb=" O LEU 0 488 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU 0 490 " --> pdb=" O VAL 0 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '0' and resid 687 through 690 removed outlier: 7.740A pdb=" N LYS 0 688 " --> pdb=" O VAL 0 505 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS 0 507 " --> pdb=" O LYS 0 688 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE 0 690 " --> pdb=" O CYS 0 507 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU 0 509 " --> pdb=" O ILE 0 690 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ALA 0 657 " --> pdb=" O GLN 0 506 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA 0 508 " --> pdb=" O ALA 0 657 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE 0 659 " --> pdb=" O ALA 0 508 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL 0 510 " --> pdb=" O PHE 0 659 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER 0 661 " --> pdb=" O VAL 0 510 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N CYS 0 512 " --> pdb=" O SER 0 661 " (cutoff:3.500A) removed outlier: 6.292A 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 5 Processing sheet with id= F, first strand: chain '1' and resid 38 through 41 removed outlier: 5.673A pdb=" N THR 1 477 " --> pdb=" O VAL 1 39 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLU 1 41 " --> pdb=" O THR 1 477 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA 1 479 " --> pdb=" O GLU 1 41 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 173 through 175 removed outlier: 6.621A pdb=" N VAL 1 204 " --> pdb=" O LEU 1 107 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU 1 70 " --> pdb=" O VAL 1 205 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR 1 207 " --> pdb=" O LEU 1 70 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR 1 72 " --> pdb=" O TYR 1 207 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER 1 453 " --> pdb=" O VAL 1 231 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE 1 233 " --> pdb=" O SER 1 453 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE 1 455 " --> pdb=" O PHE 1 233 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '1' and resid 249 through 252 Processing sheet with id= I, first strand: chain '1' and resid 490 through 493 removed outlier: 8.318A pdb=" N GLY 1 675 " --> pdb=" O CYS 1 491 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N MET 1 493 " --> pdb=" O GLY 1 675 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET 1 677 " --> pdb=" O MET 1 493 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU 1 566 " --> pdb=" O ILE 1 595 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU 1 597 " --> pdb=" O LEU 1 566 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE 1 568 " --> pdb=" O LEU 1 597 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N VAL 1 599 " --> pdb=" O PHE 1 568 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 96 through 100 Processing sheet with id= K, first strand: chain '3' and resid 271 through 273 Processing sheet with id= L, first strand: chain '3' and resid 307 through 309 removed outlier: 6.106A pdb=" N GLN 3 345 " --> pdb=" O MET 3 334 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET 3 334 " --> pdb=" O GLN 3 345 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 407 through 409 Processing sheet with id= N, first strand: chain '4' and resid 113 through 115 removed outlier: 6.384A pdb=" N SER 4 164 " --> pdb=" O HIS 4 60 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR 4 62 " --> pdb=" O SER 4 164 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU 4 166 " --> pdb=" O TYR 4 62 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL 4 64 " --> pdb=" O GLU 4 166 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU 4 168 " --> pdb=" O VAL 4 64 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASP 4 66 " --> pdb=" O LEU 4 168 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE 4 170 " --> pdb=" O ASP 4 66 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG 4 195 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE 4 169 " --> pdb=" O ARG 4 195 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER 4 197 " --> pdb=" O ILE 4 169 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE 4 171 " --> pdb=" O SER 4 197 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE 4 199 " --> pdb=" O PHE 4 171 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '4' and resid 332 through 334 Processing sheet with id= P, first strand: chain '5' and resid 67 through 69 removed outlier: 6.603A pdb=" N LYS 5 158 " --> pdb=" O LEU 5 10 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL 5 12 " --> pdb=" O LYS 5 158 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG 5 160 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL 5 14 " --> pdb=" O ARG 5 160 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU 5 162 " --> pdb=" O VAL 5 14 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASP 5 16 " --> pdb=" O LEU 5 162 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE 5 164 " --> pdb=" O ASP 5 16 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU 5 190 " --> pdb=" O ILE 5 161 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL 5 163 " --> pdb=" O LEU 5 190 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP 5 192 " --> pdb=" O VAL 5 163 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LYS 5 165 " --> pdb=" O ASP 5 192 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS 5 194 " --> pdb=" O LYS 5 165 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '6' and resid 8 through 11 Processing sheet with id= R, first strand: chain '8' and resid 77 through 81 removed outlier: 6.690A pdb=" N VAL 8 90 " --> pdb=" O LEU 8 78 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA 8 80 " --> pdb=" O SER 8 88 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER 8 88 " --> pdb=" O ALA 8 80 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG 8 30 " --> pdb=" O LYS 8 14 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS 8 14 " --> pdb=" O ARG 8 30 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '8' and resid 133 through 135 Processing sheet with id= T, first strand: chain '8' and resid 143 through 145 Processing sheet with id= U, first strand: chain 'A' and resid 86 through 89 Processing sheet with id= V, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.114A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.908A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 362 through 366 removed outlier: 3.733A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 367 through 369 removed outlier: 5.816A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.960A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.587A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= AC, first strand: chain 'A' and resid 1139 through 1142 removed outlier: 3.742A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 3.963A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 3.505A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.181A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= AH, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= AI, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= AJ, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.692A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= AL, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= AM, first strand: chain 'B' and resid 602 through 606 removed outlier: 6.238A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 747 through 751 removed outlier: 4.015A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 4.555A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 965 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N MET B 796 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN B 948 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= AQ, first strand: chain 'B' and resid 934 through 936 Processing sheet with id= AR, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id= AS, first strand: chain 'B' and resid 121 through 126 removed outlier: 6.232A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.280A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 98 through 106 removed outlier: 5.944A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 113 through 116 Processing sheet with id= AW, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.777A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.813A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AZ, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.116A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'G' and resid 142 through 147 removed outlier: 3.894A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'G' and resid 117 through 119 Processing sheet with id= BC, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.527A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'H' and resid 25 through 31 removed outlier: 5.374A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'I' and resid 24 through 28 removed outlier: 3.801A pdb=" N TYR I 44 " --> pdb=" O CYS I 39 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= BG, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= BH, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= BI, first strand: chain 'M' and resid 24 through 26 Processing sheet with id= BJ, first strand: chain 'O' and resid 170 through 173 Processing sheet with id= BK, first strand: chain 'O' and resid 281 through 283 removed outlier: 3.634A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER O 261 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU O 165 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'Q' and resid 15 through 17 removed outlier: 3.933A pdb=" N GLU Q 136 " --> pdb=" O THR Q 128 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'Q' and resid 27 through 31 removed outlier: 6.685A pdb=" N ASN Q 142 " --> pdb=" O ILE Q 28 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ALA Q 30 " --> pdb=" O ASN Q 142 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR Q 144 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS Q 109 " --> pdb=" O LEU Q 149 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'R' and resid 41 through 47 removed outlier: 10.082A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG R 113 " --> pdb=" O GLN R 86 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU R 20 " --> pdb=" O VAL R 111 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG R 113 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS R 22 " --> pdb=" O ARG R 113 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU R 115 " --> pdb=" O LYS R 22 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'R' and resid 222 through 224 removed outlier: 3.731A pdb=" N THR R 232 " --> pdb=" O ASN R 224 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'R' and resid 94 through 99 removed outlier: 6.511A pdb=" N THR R 97 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU R 106 " --> pdb=" O THR R 97 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N SER R 99 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU R 104 " --> pdb=" O SER R 99 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'U' and resid 341 through 345 removed outlier: 3.742A pdb=" N ALA U 370 " --> pdb=" O LEU U 353 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'U' and resid 363 through 367 removed outlier: 6.440A pdb=" N GLN U 338 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY U 356 " --> pdb=" O VAL U 336 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL U 336 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N MET U 358 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL U 334 " --> pdb=" O MET U 358 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'V' and resid 56 through 59 Processing sheet with id= BT, first strand: chain 'V' and resid 92 through 97 removed outlier: 6.145A pdb=" N ASN V 77 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU V 62 " --> pdb=" O ASN V 77 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'W' and resid 42 through 44 Processing sheet with id= BV, first strand: chain 'W' and resid 127 through 129 Processing sheet with id= BW, first strand: chain 'X' and resid 131 through 133 Processing sheet with id= BX, first strand: chain 'X' and resid 189 through 193 3147 hydrogen bonds defined for protein. 8709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 397 hydrogen bonds 742 hydrogen bond angles 0 basepair planarities 158 basepair parallelities 363 stacking parallelities Total time for adding SS restraints: 50.17 Time building geometry restraints manager: 33.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 37461 1.43 - 1.64: 50254 1.64 - 1.86: 671 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 88398 Sorted by residual: bond pdb=" N VAL 2 164 " pdb=" CA VAL 2 164 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.45e+00 bond pdb=" N VAL 2 314 " pdb=" CA VAL 2 314 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.78e+00 bond pdb=" N GLN 1 316 " pdb=" CA GLN 1 316 " ideal model delta sigma weight residual 1.455 1.489 -0.035 1.25e-02 6.40e+03 7.67e+00 bond pdb=" N VAL 1 314 " pdb=" CA VAL 1 314 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.61e+00 bond pdb=" N ARG M 248 " pdb=" CA ARG M 248 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.28e+00 ... (remaining 88393 not shown) Histogram of bond angle deviations from ideal: 73.49 - 85.60: 12 85.60 - 97.70: 1 97.70 - 109.81: 16643 109.81 - 121.92: 86325 121.92 - 134.02: 18218 Bond angle restraints: 121199 Sorted by residual: angle pdb=" CA LEU 1 490 " pdb=" CB LEU 1 490 " pdb=" CG LEU 1 490 " ideal model delta sigma weight residual 116.30 132.18 -15.88 3.50e+00 8.16e-02 2.06e+01 angle pdb=" O5' DT T-132 " pdb=" C5' DT T-132 " pdb=" C4' DT T-132 " ideal model delta sigma weight residual 110.80 117.12 -6.32 1.50e+00 4.44e-01 1.78e+01 angle pdb=" C TYR B 785 " pdb=" N THR B 786 " pdb=" CA THR B 786 " ideal model delta sigma weight residual 123.05 129.61 -6.56 1.57e+00 4.06e-01 1.74e+01 angle pdb=" N LYS A 910 " pdb=" CA LYS A 910 " pdb=" C LYS A 910 " ideal model delta sigma weight residual 109.81 119.02 -9.21 2.21e+00 2.05e-01 1.74e+01 angle pdb=" CA TRP B 548 " pdb=" CB TRP B 548 " pdb=" CG TRP B 548 " ideal model delta sigma weight residual 113.60 105.78 7.82 1.90e+00 2.77e-01 1.70e+01 ... (remaining 121194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 50654 34.50 - 69.00: 2089 69.00 - 103.49: 92 103.49 - 137.99: 1 137.99 - 172.49: 2 Dihedral angle restraints: 52838 sinusoidal: 24102 harmonic: 28736 Sorted by residual: dihedral pdb=" CA ILE 0 407 " pdb=" C ILE 0 407 " pdb=" N SER 0 408 " pdb=" CA SER 0 408 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ARG 1 293 " pdb=" C ARG 1 293 " pdb=" N GLU 1 294 " pdb=" CA GLU 1 294 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA VAL 2 262 " pdb=" C VAL 2 262 " pdb=" N LYS 2 263 " pdb=" CA LYS 2 263 " ideal model delta harmonic sigma weight residual -180.00 -154.58 -25.42 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 52835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 11102 0.064 - 0.128: 2267 0.128 - 0.192: 238 0.192 - 0.256: 31 0.256 - 0.321: 1 Chirality restraints: 13639 Sorted by residual: chirality pdb=" C3' DG N 10 " pdb=" C4' DG N 10 " pdb=" O3' DG N 10 " pdb=" C2' DG N 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PHE B 806 " pdb=" N PHE B 806 " pdb=" C PHE B 806 " pdb=" CB PHE B 806 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1' DG N 82 " pdb=" O4' DG N 82 " pdb=" C2' DG N 82 " pdb=" N9 DG N 82 " both_signs ideal model delta sigma weight residual False 2.42 2.17 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 13636 not shown) Planarity restraints: 14259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 4 62 " -0.004 2.00e-02 2.50e+03 4.55e-02 4.14e+01 pdb=" CG TYR 4 62 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR 4 62 " 0.066 2.00e-02 2.50e+03 pdb=" CD2 TYR 4 62 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR 4 62 " -0.065 2.00e-02 2.50e+03 pdb=" CE2 TYR 4 62 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR 4 62 " -0.064 2.00e-02 2.50e+03 pdb=" OH TYR 4 62 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 542 " 0.006 2.00e-02 2.50e+03 2.91e-02 1.69e+01 pdb=" CG TYR 1 542 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 542 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 542 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 542 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 542 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR 1 542 " 0.042 2.00e-02 2.50e+03 pdb=" OH TYR 1 542 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 151 " -0.003 2.00e-02 2.50e+03 2.75e-02 1.51e+01 pdb=" CG TYR 3 151 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 151 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 151 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 151 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 151 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR 3 151 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR 3 151 " -0.040 2.00e-02 2.50e+03 ... (remaining 14256 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 11 2.11 - 2.80: 22071 2.80 - 3.50: 127088 3.50 - 4.20: 221550 4.20 - 4.90: 376263 Nonbonded interactions: 746983 Sorted by model distance: nonbonded pdb=" C CYS 4 345 " pdb="ZN ZN 4 401 " model vdw 1.408 2.460 nonbonded pdb=" O CYS 4 345 " pdb="ZN ZN 4 401 " model vdw 1.546 2.230 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2003 " model vdw 1.593 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 1.722 2.170 nonbonded pdb=" O TYR 4 346 " pdb="ZN ZN 4 401 " model vdw 1.884 2.230 ... (remaining 746978 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' 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: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 15.830 Check model and map are aligned: 0.940 Set scattering table: 0.610 Process input model: 238.450 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.420 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: 0.030 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 266.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 88398 Z= 0.345 Angle : 0.867 15.877 121199 Z= 0.513 Chirality : 0.050 0.321 13639 Planarity : 0.009 0.118 14259 Dihedral : 16.316 172.490 34220 Min Nonbonded Distance : 1.408 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 0.06 % Allowed : 1.68 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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 (0.08), residues: 9727 helix: -0.16 (0.07), residues: 4228 sheet: -0.11 (0.14), residues: 1224 loop : -0.57 (0.09), residues: 4275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 27 HIS 0.014 0.001 HIS A 84 PHE 0.041 0.003 PHE B 895 TYR 0.066 0.006 TYR 4 62 ARG 0.030 0.004 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 371 time to evaluate : 7.139 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: 0 412 MET cc_start: 0.8711 (tpt) cc_final: 0.7712 (ptm) REVERT: 0 514 MET cc_start: 0.6132 (mmm) cc_final: 0.4414 (tpt) REVERT: 1 25 MET cc_start: 0.8729 (mmp) cc_final: 0.8394 (mmt) REVERT: 1 57 MET cc_start: 0.9104 (mtp) cc_final: 0.8825 (ptt) REVERT: 1 438 MET cc_start: 0.7756 (mtm) cc_final: 0.6651 (mpp) REVERT: 2 313 MET cc_start: 0.9181 (mmp) cc_final: 0.8785 (ptt) REVERT: 2 441 MET cc_start: 0.1998 (mmm) cc_final: 0.1554 (mmt) REVERT: 4 71 MET cc_start: 0.9324 (mmt) cc_final: 0.8676 (mmm) REVERT: 5 42 MET cc_start: -0.1902 (mtm) cc_final: -0.2154 (mtt) REVERT: 5 157 MET cc_start: 0.5732 (ttm) cc_final: 0.4938 (ptt) REVERT: 7 22 MET cc_start: 0.6941 (mmm) cc_final: 0.6403 (mpp) REVERT: 9 58 LYS cc_start: 0.2223 (mmtt) cc_final: 0.1785 (mmtm) REVERT: 9 159 ILE cc_start: -0.2616 (tt) cc_final: -0.2960 (tt) REVERT: A 248 MET cc_start: 0.9028 (mtm) cc_final: 0.8575 (mtp) REVERT: A 467 MET cc_start: 0.8705 (mpp) cc_final: 0.8366 (mpp) REVERT: A 470 MET cc_start: 0.8326 (mtm) cc_final: 0.7669 (mtp) REVERT: B 840 MET cc_start: 0.1895 (mtp) cc_final: 0.0432 (ttt) REVERT: B 1089 MET cc_start: 0.8280 (mmm) cc_final: 0.7954 (mpp) REVERT: J 48 MET cc_start: 0.8910 (mmp) cc_final: 0.8528 (mmm) REVERT: M 260 MET cc_start: 0.7613 (ttm) cc_final: 0.7305 (tpp) REVERT: O 202 MET cc_start: 0.9478 (ttm) cc_final: 0.9232 (tpt) REVERT: O 258 MET cc_start: 0.8926 (mtp) cc_final: 0.8520 (mtp) REVERT: U 51 MET cc_start: 0.6599 (mmp) cc_final: 0.5055 (mpp) REVERT: h 60 MET cc_start: 0.6642 (tpt) cc_final: 0.6150 (mtt) outliers start: 5 outliers final: 1 residues processed: 376 average time/residue: 0.8100 time to fit residues: 522.9326 Evaluate side-chains 306 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 7.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 846 optimal weight: 20.0000 chunk 759 optimal weight: 4.9990 chunk 421 optimal weight: 0.9990 chunk 259 optimal weight: 20.0000 chunk 512 optimal weight: 10.0000 chunk 405 optimal weight: 40.0000 chunk 785 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 477 optimal weight: 10.0000 chunk 584 optimal weight: 10.0000 chunk 909 optimal weight: 4.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 262 ASN 1 452 GLN ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 260 ASN ** 3 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 324 HIS A 507 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN C 66 HIS C 265 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 133 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 277 HIS ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 ASN h 85 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 88398 Z= 0.252 Angle : 0.621 12.780 121199 Z= 0.339 Chirality : 0.042 0.247 13639 Planarity : 0.004 0.069 14259 Dihedral : 19.074 167.294 15048 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.88 % Favored : 98.10 % Rotamer: Outliers : 0.04 % Allowed : 1.62 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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: 0.47 (0.08), residues: 9727 helix: 0.92 (0.08), residues: 4300 sheet: 0.13 (0.14), residues: 1180 loop : -0.14 (0.10), residues: 4247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP U 46 HIS 0.025 0.001 HIS 1 700 PHE 0.043 0.002 PHE 1 720 TYR 0.029 0.002 TYR B1048 ARG 0.014 0.001 ARG V 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 321 time to evaluate : 7.048 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: 0 514 MET cc_start: 0.6723 (mmm) cc_final: 0.5324 (tpt) REVERT: 0 536 MET cc_start: 0.9502 (mmp) cc_final: 0.9193 (mmm) REVERT: 1 57 MET cc_start: 0.9054 (mtp) cc_final: 0.8763 (ptt) REVERT: 1 438 MET cc_start: 0.7010 (mtm) cc_final: 0.5937 (mpp) REVERT: 1 478 MET cc_start: 0.3234 (mmt) cc_final: 0.3003 (mmt) REVERT: 1 724 MET cc_start: 0.8112 (mtm) cc_final: 0.7821 (mpp) REVERT: 2 313 MET cc_start: 0.9204 (mmp) cc_final: 0.8696 (ptt) REVERT: 2 441 MET cc_start: 0.1845 (mmm) cc_final: 0.1603 (mmt) REVERT: 3 228 MET cc_start: 0.5520 (tpp) cc_final: 0.4783 (tpt) REVERT: 3 254 MET cc_start: 0.5227 (ttp) cc_final: 0.4747 (ttt) REVERT: 3 334 MET cc_start: 0.2416 (mmm) cc_final: 0.2123 (mmm) REVERT: 5 42 MET cc_start: -0.1626 (mtm) cc_final: -0.1954 (mtt) REVERT: 5 157 MET cc_start: 0.5784 (ttm) cc_final: 0.4862 (ptt) REVERT: 7 22 MET cc_start: 0.7073 (mmm) cc_final: 0.6471 (mpp) REVERT: 9 58 LYS cc_start: 0.2101 (mmtt) cc_final: 0.1763 (tppt) REVERT: 9 97 MET cc_start: 0.6315 (mtm) cc_final: 0.5713 (mtm) REVERT: 9 160 VAL cc_start: 0.3352 (OUTLIER) cc_final: 0.2821 (p) REVERT: A 248 MET cc_start: 0.9051 (mtm) cc_final: 0.8607 (mtp) REVERT: A 355 MET cc_start: 0.6333 (mmp) cc_final: 0.5775 (mmt) REVERT: A 467 MET cc_start: 0.8974 (mpp) cc_final: 0.8251 (mpp) REVERT: A 470 MET cc_start: 0.8367 (mtm) cc_final: 0.7909 (mtp) REVERT: A 868 MET cc_start: 0.7307 (mtp) cc_final: 0.6972 (mtt) REVERT: A 1086 MET cc_start: 0.8952 (mmm) cc_final: 0.7927 (mmm) REVERT: A 1400 LEU cc_start: 0.9294 (tp) cc_final: 0.9063 (tt) REVERT: B 840 MET cc_start: 0.1666 (mtp) cc_final: 0.0198 (mtm) REVERT: B 954 MET cc_start: 0.8335 (mmm) cc_final: 0.8092 (tpp) REVERT: B 1089 MET cc_start: 0.8389 (mmm) cc_final: 0.8151 (mpp) REVERT: F 57 MET cc_start: 0.8006 (tmm) cc_final: 0.7726 (tmm) REVERT: M 260 MET cc_start: 0.7493 (ttm) cc_final: 0.7283 (tpp) REVERT: O 202 MET cc_start: 0.9445 (ttm) cc_final: 0.9150 (tpt) REVERT: O 258 MET cc_start: 0.8580 (mtp) cc_final: 0.8204 (mtp) REVERT: Q 29 MET cc_start: 0.8935 (mtp) cc_final: 0.8609 (mtt) REVERT: R 125 MET cc_start: 0.8434 (mmt) cc_final: 0.8060 (tpt) REVERT: U 51 MET cc_start: 0.6614 (mmp) cc_final: 0.5090 (mpp) REVERT: h 60 MET cc_start: 0.6531 (tpt) cc_final: 0.5833 (mtt) outliers start: 3 outliers final: 1 residues processed: 324 average time/residue: 0.7998 time to fit residues: 452.1130 Evaluate side-chains 302 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 300 time to evaluate : 7.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 505 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 757 optimal weight: 10.0000 chunk 619 optimal weight: 4.9990 chunk 251 optimal weight: 50.0000 chunk 911 optimal weight: 50.0000 chunk 984 optimal weight: 40.0000 chunk 811 optimal weight: 6.9990 chunk 903 optimal weight: 40.0000 chunk 310 optimal weight: 6.9990 chunk 731 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 461 HIS 0 506 GLN 0 594 GLN 0 598 HIS ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 700 HIS ** 1 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN A 531 ASN A 861 GLN A1394 ASN B 197 GLN B 486 ASN B1094 GLN C 66 HIS ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 315 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 88398 Z= 0.293 Angle : 0.600 12.050 121199 Z= 0.324 Chirality : 0.041 0.269 13639 Planarity : 0.004 0.085 14259 Dihedral : 19.215 161.962 15048 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.64 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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: 0.65 (0.08), residues: 9727 helix: 1.17 (0.08), residues: 4301 sheet: -0.05 (0.14), residues: 1205 loop : -0.07 (0.10), residues: 4221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 0 511 HIS 0.009 0.001 HIS 7 28 PHE 0.054 0.002 PHE 7 39 TYR 0.029 0.002 TYR B1048 ARG 0.009 0.001 ARG G 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 6.995 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: 0 412 MET cc_start: 0.7684 (ptm) cc_final: 0.7268 (ptm) REVERT: 0 494 MET cc_start: 0.9167 (mpp) cc_final: 0.8953 (mpp) REVERT: 0 514 MET cc_start: 0.7028 (mmm) cc_final: 0.5539 (tpt) REVERT: 0 536 MET cc_start: 0.9543 (mmp) cc_final: 0.9260 (mmm) REVERT: 1 57 MET cc_start: 0.9146 (mtp) cc_final: 0.8872 (ptt) REVERT: 1 438 MET cc_start: 0.7305 (mtm) cc_final: 0.7075 (mpp) REVERT: 1 478 MET cc_start: 0.2471 (mmt) cc_final: 0.2242 (mmt) REVERT: 1 724 MET cc_start: 0.8457 (mtm) cc_final: 0.7993 (mpp) REVERT: 2 313 MET cc_start: 0.9242 (mmp) cc_final: 0.8743 (ptt) REVERT: 2 441 MET cc_start: 0.2228 (mmm) cc_final: 0.1924 (mmt) REVERT: 3 254 MET cc_start: 0.5557 (ttp) cc_final: 0.5046 (ttt) REVERT: 3 334 MET cc_start: 0.2610 (mmm) cc_final: 0.2282 (mmm) REVERT: 5 42 MET cc_start: -0.0717 (mtm) cc_final: -0.1006 (mtt) REVERT: 5 51 MET cc_start: 0.8619 (mmp) cc_final: 0.7753 (mmt) REVERT: 5 157 MET cc_start: 0.6267 (ttm) cc_final: 0.5225 (ptt) REVERT: 7 22 MET cc_start: 0.7123 (mmm) cc_final: 0.6519 (mpp) REVERT: 7 210 MET cc_start: 0.8521 (mpp) cc_final: 0.8301 (mpp) REVERT: A 248 MET cc_start: 0.8970 (mtm) cc_final: 0.8473 (mtp) REVERT: A 355 MET cc_start: 0.6495 (mmp) cc_final: 0.6145 (mmt) REVERT: A 470 MET cc_start: 0.8475 (mtm) cc_final: 0.7702 (mtp) REVERT: A 868 MET cc_start: 0.7443 (mtp) cc_final: 0.7165 (mtt) REVERT: A 1086 MET cc_start: 0.8976 (mmm) cc_final: 0.8153 (mmm) REVERT: A 1412 MET cc_start: 0.6688 (mpp) cc_final: 0.6240 (mpp) REVERT: A 1440 MET cc_start: 0.9485 (mmm) cc_final: 0.9251 (mmm) REVERT: B 368 MET cc_start: 0.9465 (ttm) cc_final: 0.9243 (ptm) REVERT: B 840 MET cc_start: 0.1773 (mtp) cc_final: 0.0280 (mtm) REVERT: F 57 MET cc_start: 0.8093 (tmm) cc_final: 0.7757 (tmm) REVERT: H 37 MET cc_start: 0.8323 (tpp) cc_final: 0.7995 (mmm) REVERT: J 1 MET cc_start: 0.7344 (mpp) cc_final: 0.7128 (mpp) REVERT: O 202 MET cc_start: 0.9452 (ttm) cc_final: 0.9157 (tpt) REVERT: O 258 MET cc_start: 0.8533 (mtp) cc_final: 0.8118 (mtp) REVERT: Q 29 MET cc_start: 0.8921 (mtp) cc_final: 0.8601 (mtm) REVERT: U 51 MET cc_start: 0.6584 (mmp) cc_final: 0.5070 (mpp) REVERT: U 358 MET cc_start: 0.9359 (pmm) cc_final: 0.8996 (pmm) REVERT: h 60 MET cc_start: 0.6529 (tpt) cc_final: 0.5872 (mtt) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.7941 time to fit residues: 424.2241 Evaluate side-chains 295 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 6.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 900 optimal weight: 20.0000 chunk 685 optimal weight: 3.9990 chunk 473 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 435 optimal weight: 0.2980 chunk 612 optimal weight: 0.6980 chunk 914 optimal weight: 50.0000 chunk 968 optimal weight: 40.0000 chunk 477 optimal weight: 9.9990 chunk 867 optimal weight: 40.0000 chunk 261 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN B1117 HIS C 217 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 GLN d 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 88398 Z= 0.189 Angle : 0.535 13.870 121199 Z= 0.289 Chirality : 0.040 0.231 13639 Planarity : 0.004 0.042 14259 Dihedral : 19.210 165.595 15048 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.34 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 9727 helix: 1.34 (0.08), residues: 4315 sheet: -0.03 (0.15), residues: 1203 loop : -0.01 (0.10), residues: 4209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP U 46 HIS 0.007 0.001 HIS 1 612 PHE 0.030 0.001 PHE 9 30 TYR 0.029 0.001 TYR B1048 ARG 0.012 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 7.345 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: 0 412 MET cc_start: 0.7696 (ptm) cc_final: 0.7016 (ptp) REVERT: 0 514 MET cc_start: 0.7126 (mmm) cc_final: 0.5513 (tpt) REVERT: 0 536 MET cc_start: 0.9535 (mmp) cc_final: 0.9256 (mmm) REVERT: 0 650 MET cc_start: 0.4204 (ppp) cc_final: 0.3896 (ppp) REVERT: 1 25 MET cc_start: 0.7795 (mmt) cc_final: 0.7253 (mmt) REVERT: 1 57 MET cc_start: 0.9109 (mtp) cc_final: 0.8843 (ptt) REVERT: 1 478 MET cc_start: 0.2467 (mmt) cc_final: 0.2245 (mmt) REVERT: 1 620 MET cc_start: 0.8535 (mpp) cc_final: 0.8173 (mpp) REVERT: 1 677 MET cc_start: 0.9184 (pmm) cc_final: 0.8701 (pmm) REVERT: 2 313 MET cc_start: 0.9230 (mmp) cc_final: 0.8735 (ptt) REVERT: 2 441 MET cc_start: 0.2246 (mmm) cc_final: 0.1926 (mmt) REVERT: 3 57 MET cc_start: 0.1368 (ppp) cc_final: 0.1115 (ppp) REVERT: 3 228 MET cc_start: 0.5235 (ttt) cc_final: 0.3559 (ttt) REVERT: 3 254 MET cc_start: 0.5457 (ttp) cc_final: 0.4638 (ttt) REVERT: 3 334 MET cc_start: 0.2432 (mmm) cc_final: 0.2146 (mmm) REVERT: 5 42 MET cc_start: -0.0672 (mtm) cc_final: -0.1044 (mtt) REVERT: 5 51 MET cc_start: 0.8252 (mmp) cc_final: 0.7970 (mmt) REVERT: 7 22 MET cc_start: 0.7129 (mmm) cc_final: 0.6505 (mpp) REVERT: 9 58 LYS cc_start: 0.0290 (tppt) cc_final: -0.0037 (tppt) REVERT: 9 85 MET cc_start: 0.1600 (tmm) cc_final: 0.0578 (tmm) REVERT: 9 165 ARG cc_start: 0.2576 (pmt170) cc_final: 0.2350 (pmt170) REVERT: A 248 MET cc_start: 0.8929 (mtm) cc_final: 0.8400 (mtp) REVERT: A 317 MET cc_start: 0.8074 (mtt) cc_final: 0.7691 (mtt) REVERT: A 355 MET cc_start: 0.6558 (mmt) cc_final: 0.6217 (mmp) REVERT: A 470 MET cc_start: 0.8548 (mtm) cc_final: 0.8051 (mtp) REVERT: A 501 MET cc_start: 0.8831 (tpp) cc_final: 0.8585 (tpt) REVERT: A 959 MET cc_start: 0.7918 (ptp) cc_final: 0.7587 (ptm) REVERT: A 1086 MET cc_start: 0.8943 (mmm) cc_final: 0.8325 (mmm) REVERT: A 1412 MET cc_start: 0.6600 (mpp) cc_final: 0.5561 (mpp) REVERT: A 1440 MET cc_start: 0.9492 (mmm) cc_final: 0.9248 (mmm) REVERT: B 200 MET cc_start: 0.7814 (mmm) cc_final: 0.7544 (mmm) REVERT: B 368 MET cc_start: 0.9429 (ttm) cc_final: 0.9226 (ptm) REVERT: B 388 TYR cc_start: 0.6837 (m-80) cc_final: 0.6600 (m-80) REVERT: B 840 MET cc_start: 0.1821 (mtp) cc_final: 0.0714 (ttt) REVERT: B 1075 MET cc_start: 0.6872 (ptt) cc_final: 0.6628 (ptm) REVERT: F 57 MET cc_start: 0.7892 (tmm) cc_final: 0.7602 (tmm) REVERT: H 37 MET cc_start: 0.8299 (tpp) cc_final: 0.8036 (mmm) REVERT: M 32 MET cc_start: 0.8495 (mpp) cc_final: 0.8258 (mpp) REVERT: O 202 MET cc_start: 0.9424 (ttm) cc_final: 0.9134 (tpt) REVERT: Q 29 MET cc_start: 0.8921 (mtp) cc_final: 0.8652 (mtm) REVERT: U 51 MET cc_start: 0.6609 (mmp) cc_final: 0.5104 (mpp) REVERT: U 358 MET cc_start: 0.9256 (pmm) cc_final: 0.8861 (pmm) REVERT: V 1 MET cc_start: 0.0969 (ttt) cc_final: 0.0552 (ttm) REVERT: W 48 MET cc_start: 0.7789 (mpp) cc_final: 0.7135 (mpp) REVERT: h 60 MET cc_start: 0.6449 (tpt) cc_final: 0.5871 (mtt) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.8041 time to fit residues: 432.5900 Evaluate side-chains 298 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 7.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 806 optimal weight: 0.9980 chunk 549 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 721 optimal weight: 0.0980 chunk 399 optimal weight: 8.9990 chunk 826 optimal weight: 50.0000 chunk 669 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 494 optimal weight: 30.0000 chunk 869 optimal weight: 40.0000 chunk 244 optimal weight: 50.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 154 HIS ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 27 ASN 9 161 HIS A 671 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 948 GLN C 6 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 242 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 152 ASN W 143 GLN ** c 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 88398 Z= 0.239 Angle : 0.545 16.349 121199 Z= 0.293 Chirality : 0.039 0.337 13639 Planarity : 0.004 0.045 14259 Dihedral : 19.216 163.543 15048 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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: 0.85 (0.09), residues: 9727 helix: 1.39 (0.08), residues: 4316 sheet: -0.02 (0.15), residues: 1175 loop : -0.01 (0.10), residues: 4236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 9 11 HIS 0.007 0.001 HIS A 84 PHE 0.032 0.002 PHE 1 720 TYR 0.032 0.001 TYR B 766 ARG 0.008 0.000 ARG U 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 7.201 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: 0 412 MET cc_start: 0.7618 (ptm) cc_final: 0.6863 (ptp) REVERT: 0 494 MET cc_start: 0.9190 (mpp) cc_final: 0.8957 (mpp) REVERT: 0 514 MET cc_start: 0.7060 (mmm) cc_final: 0.5406 (tpt) REVERT: 0 536 MET cc_start: 0.9535 (mmp) cc_final: 0.9199 (mmm) REVERT: 0 650 MET cc_start: 0.4263 (ppp) cc_final: 0.3835 (ppp) REVERT: 1 25 MET cc_start: 0.7893 (mmt) cc_final: 0.7383 (mmt) REVERT: 1 57 MET cc_start: 0.9090 (mtp) cc_final: 0.8839 (ptt) REVERT: 1 620 MET cc_start: 0.8605 (mpp) cc_final: 0.8297 (mpp) REVERT: 2 313 MET cc_start: 0.9238 (mmp) cc_final: 0.8749 (ptt) REVERT: 2 441 MET cc_start: 0.1879 (mmm) cc_final: 0.1582 (mmt) REVERT: 3 228 MET cc_start: 0.5789 (ttt) cc_final: 0.4715 (ttm) REVERT: 3 254 MET cc_start: 0.5576 (ttp) cc_final: 0.4575 (ttt) REVERT: 3 334 MET cc_start: 0.2326 (mmm) cc_final: 0.2002 (mmm) REVERT: 3 376 MET cc_start: -0.2725 (mtm) cc_final: -0.3141 (mtm) REVERT: 5 42 MET cc_start: -0.0545 (mtm) cc_final: -0.0823 (mtt) REVERT: 5 51 MET cc_start: 0.8252 (mmp) cc_final: 0.7960 (mmt) REVERT: 5 119 MET cc_start: -0.1028 (ttt) cc_final: -0.1555 (ppp) REVERT: 7 22 MET cc_start: 0.7190 (mmm) cc_final: 0.6566 (mpp) REVERT: 7 210 MET cc_start: 0.8382 (mpp) cc_final: 0.8126 (mpp) REVERT: 9 104 ILE cc_start: 0.1492 (tp) cc_final: 0.1032 (tp) REVERT: 9 165 ARG cc_start: 0.2815 (pmt170) cc_final: 0.2507 (pmt170) REVERT: A 248 MET cc_start: 0.8949 (mtm) cc_final: 0.8513 (mtp) REVERT: A 355 MET cc_start: 0.6549 (mmt) cc_final: 0.6215 (mmp) REVERT: A 467 MET cc_start: 0.8817 (mpp) cc_final: 0.8017 (mpp) REVERT: A 470 MET cc_start: 0.8549 (mtm) cc_final: 0.7977 (mtp) REVERT: A 959 MET cc_start: 0.7997 (ptp) cc_final: 0.7616 (ptm) REVERT: A 1086 MET cc_start: 0.8901 (mmm) cc_final: 0.8570 (mmm) REVERT: A 1412 MET cc_start: 0.6847 (mpp) cc_final: 0.5779 (mpp) REVERT: B 200 MET cc_start: 0.7920 (mmm) cc_final: 0.7682 (mmm) REVERT: B 840 MET cc_start: 0.2104 (mtp) cc_final: 0.0909 (ttt) REVERT: B 1075 MET cc_start: 0.7215 (ptt) cc_final: 0.6799 (ptm) REVERT: F 57 MET cc_start: 0.7910 (tmm) cc_final: 0.7697 (tmm) REVERT: G 116 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6249 (pm20) REVERT: G 117 MET cc_start: 0.0527 (ttp) cc_final: 0.0047 (ttp) REVERT: G 131 MET cc_start: 0.7268 (mpp) cc_final: 0.6858 (mmt) REVERT: H 37 MET cc_start: 0.8424 (tpp) cc_final: 0.8172 (mmm) REVERT: Q 29 MET cc_start: 0.8940 (mtp) cc_final: 0.8729 (mtm) REVERT: U 51 MET cc_start: 0.6728 (mmp) cc_final: 0.5213 (mpp) REVERT: U 358 MET cc_start: 0.9259 (pmm) cc_final: 0.8977 (pmm) REVERT: V 1 MET cc_start: 0.0823 (ttt) cc_final: 0.0400 (ttm) REVERT: W 48 MET cc_start: 0.7869 (mpp) cc_final: 0.7180 (mpp) REVERT: h 60 MET cc_start: 0.6397 (tpt) cc_final: 0.5840 (mtt) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.8105 time to fit residues: 434.2393 Evaluate side-chains 299 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 7.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 325 optimal weight: 50.0000 chunk 872 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 568 optimal weight: 0.7980 chunk 239 optimal weight: 50.0000 chunk 969 optimal weight: 40.0000 chunk 804 optimal weight: 40.0000 chunk 448 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 320 optimal weight: 50.0000 chunk 508 optimal weight: 20.0000 overall best weight: 8.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 164 HIS ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 524 HIS ** 3 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 281 HIS ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 986 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 88398 Z= 0.321 Angle : 0.612 22.267 121199 Z= 0.326 Chirality : 0.040 0.250 13639 Planarity : 0.004 0.058 14259 Dihedral : 19.439 165.998 15048 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.26 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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: 0.64 (0.09), residues: 9727 helix: 1.26 (0.08), residues: 4316 sheet: -0.24 (0.15), residues: 1189 loop : -0.13 (0.10), residues: 4222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 9 11 HIS 0.010 0.001 HIS A 84 PHE 0.026 0.002 PHE 1 720 TYR 0.055 0.002 TYR B 752 ARG 0.036 0.001 ARG 9 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 7.114 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: 0 412 MET cc_start: 0.7777 (ptm) cc_final: 0.7429 (ptp) REVERT: 0 494 MET cc_start: 0.9266 (mpp) cc_final: 0.9047 (mpp) REVERT: 0 514 MET cc_start: 0.7141 (mmm) cc_final: 0.5515 (tpt) REVERT: 0 536 MET cc_start: 0.9519 (mmp) cc_final: 0.9209 (mmm) REVERT: 0 650 MET cc_start: 0.4450 (ppp) cc_final: 0.3949 (ppp) REVERT: 1 25 MET cc_start: 0.7977 (mmt) cc_final: 0.7416 (mmt) REVERT: 1 57 MET cc_start: 0.9034 (mtp) cc_final: 0.8816 (ptt) REVERT: 1 438 MET cc_start: 0.6448 (mpp) cc_final: 0.5997 (mpp) REVERT: 2 313 MET cc_start: 0.9269 (mmp) cc_final: 0.8793 (ptt) REVERT: 2 441 MET cc_start: 0.2071 (mmm) cc_final: 0.1729 (mmt) REVERT: 3 254 MET cc_start: 0.5546 (ttp) cc_final: 0.4551 (ttt) REVERT: 3 334 MET cc_start: 0.2685 (mmm) cc_final: 0.2349 (mmm) REVERT: 5 42 MET cc_start: -0.0018 (mtm) cc_final: -0.0353 (mtt) REVERT: 5 119 MET cc_start: -0.0747 (ttt) cc_final: -0.1414 (ppp) REVERT: 7 22 MET cc_start: 0.7371 (mmm) cc_final: 0.6682 (mpp) REVERT: 7 210 MET cc_start: 0.8441 (mpp) cc_final: 0.8227 (mpp) REVERT: 9 54 MET cc_start: 0.1176 (mmp) cc_final: 0.0773 (mtt) REVERT: 9 165 ARG cc_start: 0.2944 (pmt170) cc_final: 0.2435 (pmt170) REVERT: A 248 MET cc_start: 0.8966 (mtm) cc_final: 0.8571 (mtp) REVERT: A 355 MET cc_start: 0.6578 (mmt) cc_final: 0.6280 (mmt) REVERT: A 470 MET cc_start: 0.8497 (mtm) cc_final: 0.7992 (mtp) REVERT: A 501 MET cc_start: 0.8986 (mmt) cc_final: 0.8500 (mmt) REVERT: A 959 MET cc_start: 0.7980 (ptp) cc_final: 0.7580 (ptm) REVERT: A 1086 MET cc_start: 0.8879 (mmm) cc_final: 0.8398 (mmm) REVERT: B 155 MET cc_start: 0.7981 (ttm) cc_final: 0.7695 (ttp) REVERT: B 840 MET cc_start: 0.2504 (mtp) cc_final: 0.1242 (ttt) REVERT: D 125 GLU cc_start: 0.9292 (mm-30) cc_final: 0.9019 (pp20) REVERT: F 57 MET cc_start: 0.8113 (tmm) cc_final: 0.7666 (tmm) REVERT: G 1 MET cc_start: 0.8098 (mtt) cc_final: 0.7654 (mtt) REVERT: H 37 MET cc_start: 0.8493 (tpp) cc_final: 0.8267 (mmm) REVERT: I 23 MET cc_start: 0.9366 (tpt) cc_final: 0.8935 (tpp) REVERT: M 32 MET cc_start: 0.8563 (mpp) cc_final: 0.8286 (mpp) REVERT: U 51 MET cc_start: 0.6784 (mmp) cc_final: 0.5325 (mpp) REVERT: U 358 MET cc_start: 0.9179 (pmm) cc_final: 0.8897 (pmm) REVERT: V 1 MET cc_start: 0.1161 (ttt) cc_final: 0.0816 (ttt) REVERT: W 48 MET cc_start: 0.8058 (mpp) cc_final: 0.7419 (mpp) REVERT: h 60 MET cc_start: 0.6360 (tpt) cc_final: 0.5781 (mtt) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.7786 time to fit residues: 395.9999 Evaluate side-chains 280 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 7.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 934 optimal weight: 50.0000 chunk 109 optimal weight: 20.0000 chunk 552 optimal weight: 0.0370 chunk 707 optimal weight: 8.9990 chunk 548 optimal weight: 40.0000 chunk 816 optimal weight: 7.9990 chunk 541 optimal weight: 9.9990 chunk 965 optimal weight: 50.0000 chunk 604 optimal weight: 7.9990 chunk 588 optimal weight: 0.9990 chunk 445 optimal weight: 6.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 172 HIS ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 129 HIS A 372 ASN A 439 HIS A 671 ASN ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 ASN ** d 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 88398 Z= 0.206 Angle : 0.536 12.522 121199 Z= 0.288 Chirality : 0.039 0.199 13639 Planarity : 0.004 0.067 14259 Dihedral : 19.394 159.641 15048 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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: 9727 helix: 1.41 (0.08), residues: 4321 sheet: -0.29 (0.14), residues: 1204 loop : -0.06 (0.10), residues: 4202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 453 HIS 0.007 0.001 HIS A 809 PHE 0.028 0.002 PHE 1 720 TYR 0.042 0.001 TYR B1048 ARG 0.021 0.000 ARG 9 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 9.657 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: 0 412 MET cc_start: 0.7881 (ptm) cc_final: 0.7506 (ptp) REVERT: 0 494 MET cc_start: 0.9318 (mpp) cc_final: 0.9104 (mpp) REVERT: 0 514 MET cc_start: 0.7106 (mmm) cc_final: 0.5540 (tpt) REVERT: 0 536 MET cc_start: 0.9532 (mmp) cc_final: 0.9208 (mmm) REVERT: 0 650 MET cc_start: 0.4467 (ppp) cc_final: 0.4199 (ppp) REVERT: 1 25 MET cc_start: 0.7535 (mmt) cc_final: 0.6939 (mmt) REVERT: 1 57 MET cc_start: 0.9022 (mtp) cc_final: 0.8804 (ptt) REVERT: 1 438 MET cc_start: 0.6404 (mpp) cc_final: 0.5956 (mpp) REVERT: 1 620 MET cc_start: 0.8567 (mpp) cc_final: 0.8206 (mpp) REVERT: 1 677 MET cc_start: 0.8940 (pmm) cc_final: 0.8429 (pmm) REVERT: 2 313 MET cc_start: 0.9263 (mmp) cc_final: 0.8793 (ptt) REVERT: 2 441 MET cc_start: 0.2051 (mmm) cc_final: 0.1700 (mmt) REVERT: 3 254 MET cc_start: 0.5668 (ttp) cc_final: 0.5074 (ttp) REVERT: 3 334 MET cc_start: 0.2552 (mmm) cc_final: 0.2237 (mmm) REVERT: 5 42 MET cc_start: -0.0168 (mtm) cc_final: -0.0534 (mtt) REVERT: 5 119 MET cc_start: -0.1000 (ttt) cc_final: -0.1604 (ppp) REVERT: 5 157 MET cc_start: 0.6330 (ttm) cc_final: 0.5164 (ptt) REVERT: 7 22 MET cc_start: 0.7742 (mmm) cc_final: 0.7027 (mpp) REVERT: 7 210 MET cc_start: 0.8511 (mpp) cc_final: 0.8306 (mpp) REVERT: 9 165 ARG cc_start: 0.2863 (pmt170) cc_final: 0.2367 (pmt170) REVERT: A 238 MET cc_start: 0.8166 (ttt) cc_final: 0.7009 (mmt) REVERT: A 248 MET cc_start: 0.8922 (mtm) cc_final: 0.8602 (mtp) REVERT: A 355 MET cc_start: 0.6481 (mmt) cc_final: 0.5967 (mmp) REVERT: A 470 MET cc_start: 0.8640 (mtm) cc_final: 0.8239 (mtp) REVERT: A 501 MET cc_start: 0.8997 (mmt) cc_final: 0.8507 (mmt) REVERT: A 959 MET cc_start: 0.7856 (ptp) cc_final: 0.7445 (ptm) REVERT: A 1086 MET cc_start: 0.8835 (mmm) cc_final: 0.8432 (mmm) REVERT: A 1412 MET cc_start: 0.6674 (mpp) cc_final: 0.5841 (mpp) REVERT: B 239 MET cc_start: 0.7812 (tmm) cc_final: 0.7591 (tmm) REVERT: B 368 MET cc_start: 0.9538 (ptm) cc_final: 0.9252 (ppp) REVERT: B 529 MET cc_start: 0.8388 (mmm) cc_final: 0.7965 (mmm) REVERT: B 702 MET cc_start: 0.8391 (mmm) cc_final: 0.7739 (mmm) REVERT: B 840 MET cc_start: 0.2473 (mtp) cc_final: 0.1423 (ttt) REVERT: B 954 MET cc_start: 0.8602 (mmm) cc_final: 0.8004 (mmm) REVERT: D 39 MET cc_start: 0.9038 (ppp) cc_final: 0.8759 (ppp) REVERT: D 125 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9018 (pp20) REVERT: G 1 MET cc_start: 0.7985 (mtt) cc_final: 0.7514 (mtt) REVERT: I 23 MET cc_start: 0.9355 (tpt) cc_final: 0.8877 (tpp) REVERT: M 32 MET cc_start: 0.8454 (mpp) cc_final: 0.8254 (mpp) REVERT: U 51 MET cc_start: 0.6740 (mmp) cc_final: 0.5270 (mpp) REVERT: U 358 MET cc_start: 0.9237 (pmm) cc_final: 0.8848 (pmm) REVERT: V 1 MET cc_start: 0.1167 (ttt) cc_final: 0.0858 (ttt) REVERT: W 48 MET cc_start: 0.8007 (mpp) cc_final: 0.7354 (mpp) REVERT: X 228 MET cc_start: 0.5986 (ttt) cc_final: 0.5617 (tpp) REVERT: h 60 MET cc_start: 0.6367 (tpt) cc_final: 0.5783 (mtt) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.8594 time to fit residues: 444.4248 Evaluate side-chains 284 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 7.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 597 optimal weight: 0.9980 chunk 385 optimal weight: 8.9990 chunk 576 optimal weight: 7.9990 chunk 290 optimal weight: 50.0000 chunk 189 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 613 optimal weight: 1.9990 chunk 657 optimal weight: 8.9990 chunk 477 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 759 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS D 48 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN W 95 ASN ** d 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 88398 Z= 0.212 Angle : 0.536 12.202 121199 Z= 0.287 Chirality : 0.039 0.204 13639 Planarity : 0.004 0.064 14259 Dihedral : 19.327 158.222 15048 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.09), residues: 9727 helix: 1.46 (0.08), residues: 4322 sheet: -0.33 (0.14), residues: 1199 loop : -0.06 (0.10), residues: 4206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 1 342 HIS 0.007 0.001 HIS A 84 PHE 0.026 0.001 PHE 1 720 TYR 0.026 0.001 TYR L 41 ARG 0.019 0.000 ARG 1 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 7.331 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: 0 412 MET cc_start: 0.7891 (ptm) cc_final: 0.7493 (ptp) REVERT: 0 494 MET cc_start: 0.9331 (mpp) cc_final: 0.9112 (mpp) REVERT: 0 514 MET cc_start: 0.7284 (mmm) cc_final: 0.5824 (tpt) REVERT: 0 536 MET cc_start: 0.9519 (mmp) cc_final: 0.9203 (mmm) REVERT: 0 650 MET cc_start: 0.4525 (ppp) cc_final: 0.4208 (ppp) REVERT: 1 25 MET cc_start: 0.7592 (mmt) cc_final: 0.6984 (mmt) REVERT: 1 57 MET cc_start: 0.8981 (mtp) cc_final: 0.8765 (ptt) REVERT: 1 438 MET cc_start: 0.6370 (mpp) cc_final: 0.5932 (mpp) REVERT: 1 620 MET cc_start: 0.8575 (mpp) cc_final: 0.8170 (mpp) REVERT: 1 657 MET cc_start: 0.9432 (ppp) cc_final: 0.9223 (ppp) REVERT: 1 677 MET cc_start: 0.9314 (pmm) cc_final: 0.8410 (pmm) REVERT: 2 313 MET cc_start: 0.9268 (mmp) cc_final: 0.8812 (ptt) REVERT: 2 411 MET cc_start: 0.1626 (mpp) cc_final: 0.1342 (mpp) REVERT: 2 441 MET cc_start: 0.2067 (mmm) cc_final: 0.1757 (mmt) REVERT: 3 254 MET cc_start: 0.5699 (ttp) cc_final: 0.5069 (ttp) REVERT: 3 334 MET cc_start: 0.2651 (mmm) cc_final: 0.2324 (mmm) REVERT: 4 71 MET cc_start: 0.9530 (tpp) cc_final: 0.8902 (mmm) REVERT: 5 42 MET cc_start: -0.0218 (mtm) cc_final: -0.0531 (mtt) REVERT: 5 157 MET cc_start: 0.6263 (ttm) cc_final: 0.5108 (ptt) REVERT: 7 22 MET cc_start: 0.7738 (mmm) cc_final: 0.7055 (mpp) REVERT: 7 210 MET cc_start: 0.8393 (mpp) cc_final: 0.8170 (mpp) REVERT: 9 165 ARG cc_start: 0.2971 (pmt170) cc_final: 0.2521 (pmt170) REVERT: A 238 MET cc_start: 0.8326 (ttt) cc_final: 0.7112 (mmt) REVERT: A 248 MET cc_start: 0.8951 (mtm) cc_final: 0.8629 (mtp) REVERT: A 355 MET cc_start: 0.6472 (mmt) cc_final: 0.5901 (mmp) REVERT: A 470 MET cc_start: 0.8595 (mtm) cc_final: 0.8256 (mtp) REVERT: A 501 MET cc_start: 0.8989 (mmt) cc_final: 0.8503 (mmt) REVERT: A 959 MET cc_start: 0.7943 (ptp) cc_final: 0.7535 (ptm) REVERT: A 1086 MET cc_start: 0.8840 (mmm) cc_final: 0.8560 (mmm) REVERT: A 1440 MET cc_start: 0.9538 (mmm) cc_final: 0.9332 (mmm) REVERT: B 368 MET cc_start: 0.9523 (ptm) cc_final: 0.9173 (ppp) REVERT: B 529 MET cc_start: 0.8322 (mmm) cc_final: 0.7990 (mmm) REVERT: B 702 MET cc_start: 0.8351 (mmm) cc_final: 0.7713 (mmm) REVERT: B 840 MET cc_start: 0.2460 (mtp) cc_final: 0.1442 (ttt) REVERT: B 954 MET cc_start: 0.8515 (mmm) cc_final: 0.8034 (mmm) REVERT: D 39 MET cc_start: 0.9088 (ppp) cc_final: 0.8817 (ppp) REVERT: D 125 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9028 (pp20) REVERT: G 1 MET cc_start: 0.8011 (mtt) cc_final: 0.7589 (mtt) REVERT: R 125 MET cc_start: 0.8843 (mpp) cc_final: 0.8259 (tmm) REVERT: U 51 MET cc_start: 0.6730 (mmp) cc_final: 0.5314 (mpp) REVERT: U 358 MET cc_start: 0.9179 (pmm) cc_final: 0.8792 (pmm) REVERT: V 1 MET cc_start: 0.1357 (ttt) cc_final: 0.0874 (ttm) REVERT: X 228 MET cc_start: 0.6162 (ttt) cc_final: 0.5560 (tpp) REVERT: e 121 MET cc_start: 0.8363 (pmm) cc_final: 0.8117 (pmm) REVERT: h 60 MET cc_start: 0.6374 (tpt) cc_final: 0.5794 (mtt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.7911 time to fit residues: 400.4442 Evaluate side-chains 280 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 8.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 878 optimal weight: 50.0000 chunk 925 optimal weight: 0.5980 chunk 844 optimal weight: 9.9990 chunk 899 optimal weight: 5.9990 chunk 924 optimal weight: 40.0000 chunk 541 optimal weight: 30.0000 chunk 392 optimal weight: 0.0770 chunk 706 optimal weight: 0.0020 chunk 276 optimal weight: 50.0000 chunk 813 optimal weight: 40.0000 chunk 851 optimal weight: 0.0980 overall best weight: 1.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 377 GLN ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 221 GLN ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS D 48 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN W 95 ASN ** d 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 88398 Z= 0.146 Angle : 0.510 10.690 121199 Z= 0.273 Chirality : 0.039 0.191 13639 Planarity : 0.004 0.055 14259 Dihedral : 19.169 154.449 15048 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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: 0.93 (0.09), residues: 9727 helix: 1.54 (0.08), residues: 4335 sheet: -0.24 (0.14), residues: 1213 loop : 0.01 (0.10), residues: 4179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 0 77 HIS 0.006 0.001 HIS A 809 PHE 0.038 0.001 PHE 7 39 TYR 0.038 0.001 TYR 0 95 ARG 0.007 0.000 ARG 9 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 7.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 412 MET cc_start: 0.7880 (ptm) cc_final: 0.7460 (ptp) REVERT: 0 494 MET cc_start: 0.9350 (mpp) cc_final: 0.9122 (mpp) REVERT: 0 514 MET cc_start: 0.7159 (mmm) cc_final: 0.5692 (tpt) REVERT: 0 536 MET cc_start: 0.9493 (mmp) cc_final: 0.9174 (mmm) REVERT: 0 650 MET cc_start: 0.4303 (ppp) cc_final: 0.3967 (ppp) REVERT: 1 25 MET cc_start: 0.7514 (mmt) cc_final: 0.6907 (mmt) REVERT: 1 57 MET cc_start: 0.8927 (mtp) cc_final: 0.8717 (ptt) REVERT: 1 438 MET cc_start: 0.6355 (mpp) cc_final: 0.5935 (mpp) REVERT: 1 620 MET cc_start: 0.8494 (mpp) cc_final: 0.8246 (mpp) REVERT: 1 657 MET cc_start: 0.9395 (ppp) cc_final: 0.9189 (ppp) REVERT: 2 313 MET cc_start: 0.9261 (mmp) cc_final: 0.8801 (ptt) REVERT: 2 411 MET cc_start: 0.1547 (mpp) cc_final: 0.1294 (mpp) REVERT: 2 441 MET cc_start: 0.2102 (mmm) cc_final: 0.1759 (mmt) REVERT: 3 228 MET cc_start: 0.4767 (ttm) cc_final: 0.3838 (ttt) REVERT: 3 254 MET cc_start: 0.5561 (ttp) cc_final: 0.4921 (ttp) REVERT: 3 334 MET cc_start: 0.2616 (mmm) cc_final: 0.2327 (mmm) REVERT: 4 58 MET cc_start: 0.8514 (pmm) cc_final: 0.8292 (tpt) REVERT: 5 42 MET cc_start: -0.0670 (mtm) cc_final: -0.0998 (mtt) REVERT: 5 157 MET cc_start: 0.6232 (ttm) cc_final: 0.5118 (ptt) REVERT: 7 22 MET cc_start: 0.7499 (mmm) cc_final: 0.7035 (mpp) REVERT: 9 54 MET cc_start: 0.0757 (mpp) cc_final: 0.0400 (mmt) REVERT: 9 165 ARG cc_start: 0.2884 (pmt170) cc_final: 0.2378 (pmt170) REVERT: A 238 MET cc_start: 0.8179 (ttt) cc_final: 0.7054 (mmt) REVERT: A 248 MET cc_start: 0.8875 (mtm) cc_final: 0.8597 (mtp) REVERT: A 329 MET cc_start: 0.7507 (mmp) cc_final: 0.6891 (ttp) REVERT: A 355 MET cc_start: 0.6329 (mmt) cc_final: 0.5791 (mmp) REVERT: A 470 MET cc_start: 0.8619 (mtm) cc_final: 0.8369 (mtp) REVERT: A 501 MET cc_start: 0.9008 (mmt) cc_final: 0.8527 (mmt) REVERT: A 569 THR cc_start: 0.8633 (p) cc_final: 0.8395 (t) REVERT: A 959 MET cc_start: 0.7831 (ptp) cc_final: 0.7480 (ptm) REVERT: A 1086 MET cc_start: 0.8828 (mmm) cc_final: 0.8559 (mmm) REVERT: B 368 MET cc_start: 0.9500 (ptm) cc_final: 0.9234 (ppp) REVERT: B 529 MET cc_start: 0.8179 (mmm) cc_final: 0.7889 (mmm) REVERT: B 674 MET cc_start: 0.7697 (tpp) cc_final: 0.7037 (tpp) REVERT: B 677 MET cc_start: 0.7339 (mmt) cc_final: 0.7112 (mmt) REVERT: B 702 MET cc_start: 0.8277 (mmm) cc_final: 0.7692 (mmm) REVERT: B 840 MET cc_start: 0.2414 (mtp) cc_final: 0.1129 (ttt) REVERT: D 39 MET cc_start: 0.9098 (ppp) cc_final: 0.8838 (ppp) REVERT: D 125 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9020 (pp20) REVERT: G 1 MET cc_start: 0.7912 (mtt) cc_final: 0.6706 (mtt) REVERT: I 23 MET cc_start: 0.9251 (tpt) cc_final: 0.8559 (tpp) REVERT: R 125 MET cc_start: 0.8855 (mpp) cc_final: 0.8266 (tmm) REVERT: U 51 MET cc_start: 0.6733 (mmp) cc_final: 0.5317 (mpp) REVERT: U 358 MET cc_start: 0.9212 (pmm) cc_final: 0.8851 (pmm) REVERT: V 1 MET cc_start: 0.1381 (ttt) cc_final: 0.1032 (ttm) REVERT: X 228 MET cc_start: 0.6092 (ttt) cc_final: 0.5468 (tpp) REVERT: e 121 MET cc_start: 0.8290 (pmm) cc_final: 0.8018 (pmm) REVERT: h 60 MET cc_start: 0.6399 (tpt) cc_final: 0.5829 (mtt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.7840 time to fit residues: 409.8888 Evaluate side-chains 287 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 7.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 896 optimal weight: 20.0000 chunk 590 optimal weight: 10.0000 chunk 951 optimal weight: 50.0000 chunk 580 optimal weight: 0.6980 chunk 451 optimal weight: 2.9990 chunk 661 optimal weight: 6.9990 chunk 998 optimal weight: 50.0000 chunk 918 optimal weight: 9.9990 chunk 794 optimal weight: 40.0000 chunk 82 optimal weight: 8.9990 chunk 614 optimal weight: 0.9980 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 366 ASN ** 1 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 726 GLN ** 2 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS D 48 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 ASN W 181 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 88398 Z= 0.194 Angle : 0.529 11.065 121199 Z= 0.281 Chirality : 0.039 0.194 13639 Planarity : 0.004 0.051 14259 Dihedral : 19.147 158.237 15048 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.86 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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: 0.97 (0.09), residues: 9727 helix: 1.62 (0.08), residues: 4327 sheet: -0.30 (0.14), residues: 1237 loop : 0.01 (0.10), residues: 4163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 453 HIS 0.008 0.001 HIS B 970 PHE 0.032 0.001 PHE 1 720 TYR 0.033 0.001 TYR B1048 ARG 0.016 0.000 ARG 9 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19454 Ramachandran restraints generated. 9727 Oldfield, 0 Emsley, 9727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 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: 0 412 MET cc_start: 0.7968 (ptm) cc_final: 0.7567 (ptp) REVERT: 0 494 MET cc_start: 0.9309 (mpp) cc_final: 0.9054 (mpp) REVERT: 0 514 MET cc_start: 0.7068 (mmm) cc_final: 0.5551 (tpt) REVERT: 0 536 MET cc_start: 0.9498 (mmp) cc_final: 0.9182 (mmm) REVERT: 0 650 MET cc_start: 0.4405 (ppp) cc_final: 0.4043 (ppp) REVERT: 1 25 MET cc_start: 0.7573 (mmt) cc_final: 0.6969 (mmt) REVERT: 1 438 MET cc_start: 0.6696 (mpp) cc_final: 0.6290 (mpp) REVERT: 1 620 MET cc_start: 0.8560 (mpp) cc_final: 0.8304 (mpp) REVERT: 1 657 MET cc_start: 0.9392 (ppp) cc_final: 0.9191 (ppp) REVERT: 2 313 MET cc_start: 0.9263 (mmp) cc_final: 0.8826 (ptt) REVERT: 2 411 MET cc_start: 0.1230 (mpp) cc_final: 0.0988 (mpp) REVERT: 2 441 MET cc_start: 0.2200 (mmm) cc_final: 0.1883 (mmt) REVERT: 3 228 MET cc_start: 0.4399 (ttm) cc_final: 0.3645 (ttm) REVERT: 3 254 MET cc_start: 0.5648 (ttp) cc_final: 0.5056 (ttp) REVERT: 3 334 MET cc_start: 0.2619 (mmm) cc_final: 0.2322 (mmm) REVERT: 5 42 MET cc_start: -0.0504 (mtm) cc_final: -0.0847 (mtt) REVERT: 5 157 MET cc_start: 0.6137 (ttm) cc_final: 0.5073 (ptt) REVERT: 7 22 MET cc_start: 0.7391 (mmm) cc_final: 0.6889 (mpp) REVERT: 9 165 ARG cc_start: 0.2910 (pmt170) cc_final: 0.2444 (pmt170) REVERT: A 238 MET cc_start: 0.8322 (ttt) cc_final: 0.7140 (mmt) REVERT: A 248 MET cc_start: 0.8921 (mtm) cc_final: 0.8621 (mtp) REVERT: A 329 MET cc_start: 0.7514 (mmp) cc_final: 0.6832 (ttp) REVERT: A 355 MET cc_start: 0.6404 (mmt) cc_final: 0.5856 (mmp) REVERT: A 470 MET cc_start: 0.8578 (mtm) cc_final: 0.8210 (mtp) REVERT: A 501 MET cc_start: 0.9007 (mmt) cc_final: 0.8480 (mmt) REVERT: A 569 THR cc_start: 0.8696 (p) cc_final: 0.8437 (t) REVERT: A 959 MET cc_start: 0.7938 (ptp) cc_final: 0.7523 (ptm) REVERT: A 1086 MET cc_start: 0.8861 (mmm) cc_final: 0.8608 (mmm) REVERT: B 239 MET cc_start: 0.7803 (tmm) cc_final: 0.7564 (tmm) REVERT: B 368 MET cc_start: 0.9508 (ptm) cc_final: 0.9246 (ppp) REVERT: B 529 MET cc_start: 0.8313 (mmm) cc_final: 0.8038 (mmm) REVERT: B 674 MET cc_start: 0.7880 (tpp) cc_final: 0.7094 (tpp) REVERT: B 677 MET cc_start: 0.7315 (mmt) cc_final: 0.7029 (mmt) REVERT: B 702 MET cc_start: 0.8354 (mmm) cc_final: 0.7805 (mmm) REVERT: B 840 MET cc_start: 0.2112 (mtp) cc_final: 0.1097 (ttt) REVERT: D 39 MET cc_start: 0.9148 (ppp) cc_final: 0.8887 (ppp) REVERT: D 125 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9024 (pp20) REVERT: E 18 MET cc_start: 0.7379 (ptp) cc_final: 0.6993 (ptt) REVERT: G 1 MET cc_start: 0.7961 (mtt) cc_final: 0.6782 (mtt) REVERT: I 23 MET cc_start: 0.9339 (tpt) cc_final: 0.8616 (tpp) REVERT: Q 29 MET cc_start: 0.8827 (mtp) cc_final: 0.8546 (mtt) REVERT: R 125 MET cc_start: 0.8863 (mpp) cc_final: 0.8257 (tmm) REVERT: U 51 MET cc_start: 0.6715 (mmp) cc_final: 0.5327 (mpp) REVERT: U 358 MET cc_start: 0.9252 (pmm) cc_final: 0.8833 (pmm) REVERT: V 1 MET cc_start: 0.1519 (ttt) cc_final: 0.1185 (ttm) REVERT: X 228 MET cc_start: 0.6288 (ttt) cc_final: 0.5497 (tpp) REVERT: e 121 MET cc_start: 0.8357 (pmm) cc_final: 0.8073 (pmm) REVERT: h 60 MET cc_start: 0.6426 (tpt) cc_final: 0.5882 (mtt) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.7835 time to fit residues: 385.9442 Evaluate side-chains 274 residues out of total 8669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 7.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1002 random chunks: chunk 487 optimal weight: 8.9990 chunk 631 optimal weight: 7.9990 chunk 846 optimal weight: 6.9990 chunk 243 optimal weight: 40.0000 chunk 732 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 220 optimal weight: 40.0000 chunk 796 optimal weight: 70.0000 chunk 333 optimal weight: 50.0000 chunk 817 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 377 GLN ** 1 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 613 HIS ** 1 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS D 48 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN W 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.059133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.042681 restraints weight = 1557836.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.042105 restraints weight = 1062211.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.041835 restraints weight = 863533.831| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 88398 Z= 0.200 Angle : 0.530 11.553 121199 Z= 0.282 Chirality : 0.039 0.252 13639 Planarity : 0.004 0.072 14259 Dihedral : 19.182 161.493 15048 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % 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: 0.97 (0.09), residues: 9727 helix: 1.63 (0.08), residues: 4329 sheet: -0.30 (0.14), residues: 1241 loop : -0.01 (0.10), residues: 4157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 453 HIS 0.006 0.001 HIS A 84 PHE 0.026 0.001 PHE 7 39 TYR 0.032 0.001 TYR B1048 ARG 0.014 0.000 ARG 9 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13697.72 seconds wall clock time: 245 minutes 17.01 seconds (14717.01 seconds total)