Starting phenix.real_space_refine (version: dev) on Thu Dec 22 16:06:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwd_14997/12_2022/7zwd_14997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwd_14997/12_2022/7zwd_14997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwd_14997/12_2022/7zwd_14997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwd_14997/12_2022/7zwd_14997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwd_14997/12_2022/7zwd_14997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zwd_14997/12_2022/7zwd_14997.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 146": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 120": "OE1" <-> "OE2" Residue "M ARG 127": "NH1" <-> "NH2" Residue "M PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 157": "OD1" <-> "OD2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 171": "OE1" <-> "OE2" Residue "M GLU 203": "OE1" <-> "OE2" Residue "M PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 243": "OD1" <-> "OD2" Residue "M TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 273": "OE1" <-> "OE2" Residue "M ASP 276": "OD1" <-> "OD2" Residue "M TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 307": "OD1" <-> "OD2" Residue "O ASP 179": "OD1" <-> "OD2" Residue "O GLU 191": "OE1" <-> "OE2" Residue "O TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 196": "NH1" <-> "NH2" Residue "O ARG 203": "NH1" <-> "NH2" Residue "O ARG 208": "NH1" <-> "NH2" Residue "O PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 228": "OE1" <-> "OE2" Residue "O ARG 235": "NH1" <-> "NH2" Residue "O PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 269": "NH1" <-> "NH2" Residue "O PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 284": "OE1" <-> "OE2" Residue "O GLU 286": "OE1" <-> "OE2" Residue "O TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 294": "NH1" <-> "NH2" Residue "O ARG 299": "NH1" <-> "NH2" Residue "O ARG 318": "NH1" <-> "NH2" Residue "O GLU 320": "OE1" <-> "OE2" Residue "O GLU 326": "OE1" <-> "OE2" Residue "O ARG 336": "NH1" <-> "NH2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 35": "OD1" <-> "OD2" Residue "U ASP 340": "OD1" <-> "OD2" Residue "U ARG 363": "NH1" <-> "NH2" Residue "U TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 20": "OD1" <-> "OD2" Residue "V GLU 21": "OE1" <-> "OE2" Residue "V ASP 78": "OD1" <-> "OD2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 10": "OD1" <-> "OD2" Residue "a GLU 12": "OE1" <-> "OE2" Residue "a ASP 22": "OD1" <-> "OD2" Residue "a ASP 28": "OD1" <-> "OD2" Residue "a GLU 50": "OE1" <-> "OE2" Residue "a TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 105": "OD1" <-> "OD2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 121": "OD1" <-> "OD2" Residue "a TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 179": "OE1" <-> "OE2" Residue "a ASP 185": "OD1" <-> "OD2" Residue "a PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 33": "OE1" <-> "OE2" Residue "b PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 65": "OE1" <-> "OE2" Residue "b ASP 78": "OD1" <-> "OD2" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b ASP 89": "OD1" <-> "OD2" Residue "b ASP 91": "OD1" <-> "OD2" Residue "b GLU 95": "OE1" <-> "OE2" Residue "b GLU 138": "OE1" <-> "OE2" Residue "b ARG 140": "NH1" <-> "NH2" Residue "b GLU 141": "OE1" <-> "OE2" Residue "b TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 217": "OD1" <-> "OD2" Residue "b PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 276": "OE1" <-> "OE2" Residue "b GLU 279": "OE1" <-> "OE2" Residue "b PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 318": "OE1" <-> "OE2" Residue "b ASP 325": "OD1" <-> "OD2" Residue "b ASP 369": "OD1" <-> "OD2" Residue "b GLU 374": "OE1" <-> "OE2" Residue "b PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 392": "OE1" <-> "OE2" Residue "b PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 81": "OE1" <-> "OE2" Residue "c ASP 82": "OD1" <-> "OD2" Residue "c GLU 84": "OE1" <-> "OE2" Residue "c GLU 95": "OE1" <-> "OE2" Residue "c GLU 116": "OE1" <-> "OE2" Residue "c ASP 121": "OD1" <-> "OD2" Residue "c TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 152": "OD1" <-> "OD2" Residue "c GLU 178": "OE1" <-> "OE2" Residue "c ASP 199": "OD1" <-> "OD2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c GLU 225": "OE1" <-> "OE2" Residue "c GLU 239": "OE1" <-> "OE2" Residue "c ASP 244": "OD1" <-> "OD2" Residue "c GLU 251": "OE1" <-> "OE2" Residue "c ARG 257": "NH1" <-> "NH2" Residue "c ASP 259": "OD1" <-> "OD2" Residue "c GLU 272": "OE1" <-> "OE2" Residue "c GLU 279": "OE1" <-> "OE2" Residue "c GLU 300": "OE1" <-> "OE2" Residue "c GLU 301": "OE1" <-> "OE2" Residue "c GLU 323": "OE1" <-> "OE2" Residue "c GLU 352": "OE1" <-> "OE2" Residue "c TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 396": "OD1" <-> "OD2" Residue "d GLU 7": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d GLU 13": "OE1" <-> "OE2" Residue "d GLU 32": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 49279 Number of models: 1 Model: "" Number of chains: 32 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: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1879 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain breaks: 1 Chain: "N" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1351 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} 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: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1355 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "U" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 735 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1807 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "b" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2978 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2516 Classifications: {'peptide': 303} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 292} Chain breaks: 1 Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 424 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 61.471 103.596 133.542 1.00188.40 S ATOM 486 SG CYS A 74 61.510 102.604 137.229 1.00187.19 S ATOM 533 SG CYS A 81 64.568 102.198 134.942 1.00176.19 S ATOM 768 SG CYS A 111 54.172 55.496 134.038 1.00203.62 S ATOM 796 SG CYS A 114 51.641 56.113 136.585 1.00201.77 S ATOM 1109 SG CYS A 154 53.566 52.872 136.676 1.00192.62 S ATOM 1132 SG CYS A 184 51.032 53.527 133.909 1.00189.72 S ATOM 19919 SG CYS B1119 56.777 91.430 147.322 1.00181.82 S ATOM 19941 SG CYS B1122 57.934 89.128 144.529 1.00176.36 S ATOM 20056 SG CYS B1137 56.292 92.409 143.652 1.00189.01 S ATOM 20077 SG CYS B1140 54.403 89.428 145.232 1.00187.31 S ATOM 21044 SG CYS C 88 111.440 146.537 140.365 1.00 60.70 S ATOM 21057 SG CYS C 90 109.541 145.138 137.199 1.00 73.15 S ATOM 21092 SG CYS C 94 112.326 147.543 137.039 1.00 55.94 S ATOM 21114 SG CYS C 97 112.831 143.991 138.059 1.00 46.55 S ATOM 28400 SG CYS I 17 117.120 27.821 107.300 1.00127.85 S ATOM 28424 SG CYS I 20 114.367 30.275 106.514 1.00131.01 S ATOM 28585 SG CYS I 39 114.236 28.270 109.652 1.00141.78 S ATOM 28610 SG CYS I 42 113.803 26.652 106.034 1.00142.01 S ATOM 28962 SG CYS I 86 151.659 48.682 125.804 1.00 91.73 S ATOM 28986 SG CYS I 89 154.241 49.808 123.287 1.00 99.89 S ATOM 29190 SG CYS I 114 151.262 51.878 123.861 1.00 76.44 S ATOM 29225 SG CYS I 119 151.014 48.575 122.085 1.00 88.88 S ATOM 29336 SG CYS J 7 132.486 119.384 138.099 1.00 24.20 S ATOM 29360 SG CYS J 10 133.536 122.001 140.562 1.00 31.61 S ATOM 29624 SG CYS J 44 134.778 118.416 140.869 1.00 25.25 S ATOM 29630 SG CYS J 45 135.964 120.817 138.387 1.00 25.98 S ATOM 30750 SG CYS L 19 109.635 118.726 100.734 1.00 55.89 S ATOM 30769 SG CYS L 22 111.466 121.390 98.833 1.00 62.37 S ATOM 30886 SG CYS L 36 107.840 120.852 98.197 1.00 62.39 S ATOM 30912 SG CYS L 39 111.030 117.883 97.100 1.00 67.02 S ATOM 31094 SG CYS M 15 69.170 123.434 138.532 1.00148.54 S ATOM 31241 SG CYS M 34 72.301 124.741 136.681 1.00142.70 S ATOM 31263 SG CYS M 37 71.891 125.001 141.193 1.00143.59 S ATOM 44739 SG CYS b 221 113.127 96.511 25.200 1.00200.08 S ATOM 45536 SG CYS b 317 110.027 96.445 26.315 1.00197.58 S ATOM 45858 SG CYS b 354 125.602 75.363 26.856 1.00200.90 S ATOM 45882 SG CYS b 357 129.558 74.876 26.425 1.00200.28 S ATOM 46073 SG CYS b 380 126.874 76.111 23.771 1.00196.40 S ATOM 46094 SG CYS b 383 127.248 72.912 25.061 1.00196.18 S Time building chain proxies: 27.50, per 1000 atoms: 0.56 Number of scatterers: 49279 At special positions: 0 Unit cell: (169.05, 193.2, 223.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 11 29.99 S 275 16.00 P 132 15.00 Mg 1 11.99 O 9472 8.00 N 8660 7.00 C 30728 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: 19.56 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " 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 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 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 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 313 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 221 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 317 " pdb="ZN ZN b 501 " - pdb=" NE2 HIS b 319 " pdb=" ZN b 502 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 354 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 383 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 380 " pdb="ZN ZN b 502 " - pdb=" SG CYS b 357 " Number of angles added : 56 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10946 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 53 sheets defined 43.0% alpha, 14.5% beta 58 base pairs and 118 stacking pairs defined. Time for finding SS restraints: 15.88 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.613A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.774A pdb=" N GLU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.519A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.584A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.531A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.994A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.517A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 8.135A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.671A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.553A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 857 removed outlier: 3.641A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 869 removed outlier: 3.627A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.970A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.534A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.381A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.512A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 4.298A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 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 1186 through 1197 removed outlier: 4.104A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 4.049A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A1232 " --> pdb=" O MET A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1267 Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.788A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 4.574A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.517A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.700A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.477A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.772A pdb=" N GLY B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.680A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.529A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.773A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 489 through 496 removed outlier: 3.789A pdb=" N LYS B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.818A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.886A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.633A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.703A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.636A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.502A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.943A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.535A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.539A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.536A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.604A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.590A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.866A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.893A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 6.039A pdb=" N THR E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.540A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 3.889A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.974A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.520A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.692A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.859A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 47 through 52 Processing helix chain 'M' and resid 117 through 129 removed outlier: 3.591A pdb=" N ARG M 127 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.537A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 172 removed outlier: 3.586A pdb=" N GLY M 172 " --> pdb=" O CYS M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 180 Processing helix chain 'M' and resid 187 through 202 Processing helix chain 'M' and resid 210 through 213 Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.810A pdb=" N SER M 220 " --> pdb=" O SER M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 265 Processing helix chain 'M' and resid 270 through 279 removed outlier: 3.502A pdb=" N ILE M 274 " --> pdb=" O THR M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 291 removed outlier: 3.569A pdb=" N LEU M 291 " --> pdb=" O GLN M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.655A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 244 Processing helix chain 'O' and resid 269 through 277 Processing helix chain 'O' and resid 317 through 335 removed outlier: 3.533A pdb=" N ILE O 321 " --> pdb=" O VAL O 317 " (cutoff:3.500A) Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 34 through 36 No H-bonds generated for 'chain 'Q' and resid 34 through 36' Processing helix chain 'Q' and resid 156 through 166 removed outlier: 3.853A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 180 removed outlier: 3.595A pdb=" N ILE Q 176 " --> pdb=" O ASN Q 172 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN Q 178 " --> pdb=" O PHE Q 174 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG Q 180 " --> pdb=" O ILE Q 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 15 Processing helix chain 'R' and resid 24 through 35 removed outlier: 3.540A pdb=" N SER R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA R 34 " --> pdb=" O GLN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'R' and resid 121 through 136 removed outlier: 4.008A pdb=" N MET R 125 " --> pdb=" O SER R 121 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 173 Processing helix chain 'R' and resid 179 through 192 removed outlier: 3.892A pdb=" N GLU R 192 " --> pdb=" O PHE R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 207 Processing helix chain 'R' and resid 209 through 221 removed outlier: 3.547A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 33 removed outlier: 5.073A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 50 removed outlier: 3.641A pdb=" N LEU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 51 Processing helix chain 'a' and resid 6 through 20 Processing helix chain 'a' and resid 25 through 37 removed outlier: 3.738A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 42 removed outlier: 3.679A pdb=" N PHE a 42 " --> pdb=" O GLY a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 67 Processing helix chain 'a' and resid 71 through 88 Processing helix chain 'a' and resid 103 through 117 Processing helix chain 'a' and resid 119 through 132 Processing helix chain 'a' and resid 166 through 172 removed outlier: 3.957A pdb=" N LYS a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 195 removed outlier: 3.689A pdb=" N VAL a 193 " --> pdb=" O ASN a 189 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER a 195 " --> pdb=" O LYS a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 232 removed outlier: 4.537A pdb=" N ASP a 214 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 55 Processing helix chain 'b' and resid 77 through 91 removed outlier: 3.646A pdb=" N ARG b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 104 Processing helix chain 'b' and resid 127 through 144 Processing helix chain 'b' and resid 150 through 161 Processing helix chain 'b' and resid 192 through 197 Processing helix chain 'b' and resid 221 through 225 Processing helix chain 'b' and resid 242 through 247 removed outlier: 3.658A pdb=" N LEU b 246 " --> pdb=" O ILE b 242 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR b 247 " --> pdb=" O SER b 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 242 through 247' Processing helix chain 'b' and resid 270 through 280 removed outlier: 4.263A pdb=" N ILE b 274 " --> pdb=" O LEU b 270 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 300 Processing helix chain 'b' and resid 380 through 389 removed outlier: 3.800A pdb=" N TYR b 389 " --> pdb=" O ARG b 385 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 123 Processing helix chain 'c' and resid 142 through 146 Processing helix chain 'c' and resid 162 through 171 Processing helix chain 'c' and resid 185 through 221 removed outlier: 3.820A pdb=" N ARG c 193 " --> pdb=" O LYS c 189 " (cutoff:3.500A) Proline residue: c 207 - end of helix removed outlier: 3.584A pdb=" N LYS c 221 " --> pdb=" O GLN c 217 " (cutoff:3.500A) Processing helix chain 'c' and resid 225 through 247 Processing helix chain 'c' and resid 249 through 255 removed outlier: 3.967A pdb=" N GLY c 255 " --> pdb=" O GLU c 251 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 267 Processing helix chain 'c' and resid 276 through 287 Processing helix chain 'c' and resid 298 through 313 Processing helix chain 'c' and resid 316 through 324 Processing helix chain 'c' and resid 329 through 340 Processing helix chain 'c' and resid 350 through 365 Processing helix chain 'c' and resid 371 through 377 removed outlier: 4.182A pdb=" N TYR c 377 " --> pdb=" O ARG c 373 " (cutoff:3.500A) Processing helix chain 'c' and resid 383 through 394 Processing helix chain 'd' and resid 2 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 6.665A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.907A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 266 removed outlier: 3.715A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.872A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.633A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.009A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.674A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 581 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 579 through 581 current: chain 'H' and resid 25 through 32 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 38 through 44 current: chain 'H' and resid 111 through 118 Processing sheet with id=AB2, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.810A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB4, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB6, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB7, first strand: chain 'A' and resid 1307 through 1310 Processing sheet with id=AB8, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 7.233A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.297A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC2, first strand: chain 'A' and resid 1471 through 1475 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 115 through 119 current: chain 'G' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 54 current: chain 'G' and resid 66 through 77 Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.241A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.393A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.502A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 632 through 633 current: chain 'B' and resid 695 through 696 Processing sheet with id=AC9, first strand: chain 'B' and resid 550 through 552 removed outlier: 5.506A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.631A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD3, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.003A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.728A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1113 through 1119 removed outlier: 3.529A pdb=" N TYR B1114 " --> pdb=" O MET B1151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.736A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 121 through 122 removed outlier: 7.011A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.501A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.755A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.816A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 84 through 92 removed outlier: 7.015A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG G 151 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 160 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AE6, first strand: chain 'I' and resid 24 through 29 removed outlier: 3.723A pdb=" N ASP I 29 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR I 44 " --> pdb=" O CYS I 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'M' and resid 24 through 26 removed outlier: 3.579A pdb=" N MET M 32 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 200 through 203 removed outlier: 3.635A pdb=" N GLY O 223 " --> pdb=" O ILE O 168 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE O 168 " --> pdb=" O GLY O 223 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU O 165 " --> pdb=" O VAL O 259 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL O 259 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN O 167 " --> pdb=" O ASN O 257 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN O 257 " --> pdb=" O ASN O 167 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL O 169 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE O 255 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR O 171 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE O 253 " --> pdb=" O THR O 171 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N MET O 258 " --> pdb=" O GLY O 314 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY O 314 " --> pdb=" O MET O 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 11 through 17 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 11 through 17 current: chain 'Q' and resid 98 through 102 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 109 through 114 current: chain 'Q' and resid 135 through 139 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 135 through 139 current: chain 'R' and resid 52 through 58 removed outlier: 10.763A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 81 through 86 current: chain 'R' and resid 104 through 116 Processing sheet with id=AF3, first strand: chain 'R' and resid 222 through 224 removed outlier: 3.534A pdb=" N VAL R 222 " --> pdb=" O GLU R 234 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 334 through 344 removed outlier: 6.678A pdb=" N VAL U 334 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET U 358 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL U 336 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY U 356 " --> pdb=" O VAL U 336 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN U 338 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N HIS U 352 " --> pdb=" O ASP U 340 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE U 342 " --> pdb=" O LYS U 350 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS U 350 " --> pdb=" O ILE U 342 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG U 344 " --> pdb=" O LYS U 348 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS U 348 " --> pdb=" O ARG U 344 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 363 through 367 current: chain 'V' and resid 55 through 64 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 55 through 64 current: chain 'V' and resid 71 through 82 removed outlier: 6.766A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 97 through 99 removed outlier: 6.138A pdb=" N ILE a 97 " --> pdb=" O HIS a 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'b' and resid 42 through 43 Processing sheet with id=AF7, first strand: chain 'b' and resid 290 through 291 removed outlier: 6.626A pdb=" N PHE b 258 " --> pdb=" O ALA b 291 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE b 321 " --> pdb=" O LEU b 187 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU b 187 " --> pdb=" O ILE b 321 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE b 323 " --> pdb=" O ASN b 185 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN b 185 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP b 325 " --> pdb=" O SER b 183 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR b 203 " --> pdb=" O ILE b 344 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU b 342 " --> pdb=" O LEU b 205 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 377 through 379 1988 hydrogen bonds defined for protein. 5586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 276 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 118 stacking parallelities Total time for adding SS restraints: 28.22 Time building geometry restraints manager: 21.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15888 1.34 - 1.46: 11126 1.46 - 1.58: 22781 1.58 - 1.70: 262 1.70 - 1.83: 432 Bond restraints: 50489 Sorted by residual: bond pdb=" C1' DG T 7 " pdb=" N9 DG T 7 " ideal model delta sigma weight residual 1.460 1.368 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1' DA T -13 " pdb=" N9 DA T -13 " ideal model delta sigma weight residual 1.460 1.377 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" O3' DA N 8 " pdb=" P DG N 9 " ideal model delta sigma weight residual 1.607 1.662 -0.055 1.50e-02 4.44e+03 1.32e+01 bond pdb=" O3' DC T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.31e+01 bond pdb=" O3' DA N -2 " pdb=" P DT N -1 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.50e-02 4.44e+03 1.20e+01 ... (remaining 50484 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.15: 1371 105.15 - 112.39: 26063 112.39 - 119.64: 16600 119.64 - 126.89: 23838 126.89 - 134.13: 854 Bond angle restraints: 68726 Sorted by residual: angle pdb=" O3' DT T 5 " pdb=" C3' DT T 5 " pdb=" C2' DT T 5 " ideal model delta sigma weight residual 111.50 101.99 9.51 1.50e+00 4.44e-01 4.02e+01 angle pdb=" N ALA b 172 " pdb=" CA ALA b 172 " pdb=" C ALA b 172 " ideal model delta sigma weight residual 114.31 107.28 7.03 1.29e+00 6.01e-01 2.97e+01 angle pdb=" C VAL b 120 " pdb=" N ILE b 121 " pdb=" CA ILE b 121 " ideal model delta sigma weight residual 120.24 123.61 -3.37 6.30e-01 2.52e+00 2.86e+01 angle pdb=" O3' DG N -12 " pdb=" C3' DG N -12 " pdb=" C2' DG N -12 " ideal model delta sigma weight residual 111.50 119.27 -7.77 1.50e+00 4.44e-01 2.69e+01 angle pdb=" N ASN V 8 " pdb=" CA ASN V 8 " pdb=" C ASN V 8 " ideal model delta sigma weight residual 114.75 108.86 5.89 1.26e+00 6.30e-01 2.18e+01 ... (remaining 68721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.26: 28469 28.26 - 56.52: 1717 56.52 - 84.77: 211 84.77 - 113.03: 23 113.03 - 141.29: 1 Dihedral angle restraints: 30421 sinusoidal: 13533 harmonic: 16888 Sorted by residual: dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA LYS b 346 " pdb=" C LYS b 346 " pdb=" N HIS b 347 " pdb=" CA HIS b 347 " ideal model delta harmonic sigma weight residual 180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 30418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 7030 0.087 - 0.174: 563 0.174 - 0.261: 13 0.261 - 0.348: 3 0.348 - 0.435: 1 Chirality restraints: 7610 Sorted by residual: chirality pdb=" C3' DG N -12 " pdb=" C4' DG N -12 " pdb=" O3' DG N -12 " pdb=" C2' DG N -12 " both_signs ideal model delta sigma weight residual False -2.66 -2.23 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" P DC N -7 " pdb=" OP1 DC N -7 " pdb=" OP2 DC N -7 " pdb=" O5' DC N -7 " both_signs ideal model delta sigma weight residual True 2.35 -2.63 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA TYR b 340 " pdb=" N TYR b 340 " pdb=" C TYR b 340 " pdb=" CB TYR b 340 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 7607 not shown) Planarity restraints: 8447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 172 " -0.031 2.00e-02 2.50e+03 6.17e-02 3.81e+01 pdb=" C ASP R 172 " 0.107 2.00e-02 2.50e+03 pdb=" O ASP R 172 " -0.041 2.00e-02 2.50e+03 pdb=" N GLY R 173 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 340 " -0.020 2.00e-02 2.50e+03 1.47e-02 4.35e+00 pdb=" CG TYR b 340 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR b 340 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR b 340 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR b 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR b 340 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR b 340 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR b 340 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 7 " -0.022 2.00e-02 2.50e+03 1.28e-02 3.69e+00 pdb=" N1 DC N 7 " 0.028 2.00e-02 2.50e+03 pdb=" C2 DC N 7 " 0.005 2.00e-02 2.50e+03 pdb=" O2 DC N 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC N 7 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC N 7 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC N 7 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC N 7 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC N 7 " 0.006 2.00e-02 2.50e+03 ... (remaining 8444 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 43 2.23 - 2.90: 19170 2.90 - 3.56: 72583 3.56 - 4.23: 125128 4.23 - 4.90: 208743 Nonbonded interactions: 425667 Sorted by model distance: nonbonded pdb=" OP2 DG N 12 " pdb=" NZ LYS R 169 " model vdw 1.559 2.520 nonbonded pdb=" O GLU B 432 " pdb=" OH TYR R 153 " model vdw 1.655 2.440 nonbonded pdb=" NZ LYS B 820 " pdb=" NH2 ARG M 137 " model vdw 1.697 3.200 nonbonded pdb=" NH2 ARG B 438 " pdb=" OD1 ASP M 126 " model vdw 1.762 2.520 nonbonded pdb=" OH TYR B 814 " pdb=" OE1 GLU B 900 " model vdw 1.959 2.440 ... (remaining 425662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 11 6.06 5 P 132 5.49 5 Mg 1 5.21 5 S 275 5.16 5 C 30728 2.51 5 N 8660 2.21 5 O 9472 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.030 Extract box with map and model: 17.350 Check model and map are aligned: 0.700 Convert atoms to be neutral: 0.400 Process input model: 151.120 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 0.092 50489 Z= 0.327 Angle : 0.619 9.508 68726 Z= 0.368 Chirality : 0.044 0.435 7610 Planarity : 0.003 0.062 8447 Dihedral : 17.085 141.290 19475 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % 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: 0.25 (0.11), residues: 5715 helix: 0.91 (0.11), residues: 2191 sheet: 0.44 (0.18), residues: 826 loop : -0.47 (0.12), residues: 2698 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 965 time to evaluate : 5.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 8 residues processed: 966 average time/residue: 1.6190 time to fit residues: 1967.0423 Evaluate side-chains 523 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 515 time to evaluate : 5.669 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 5 average time/residue: 0.7810 time to fit residues: 13.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 488 optimal weight: 30.0000 chunk 438 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 453 optimal weight: 8.9990 chunk 175 optimal weight: 0.5980 chunk 275 optimal weight: 0.3980 chunk 337 optimal weight: 0.5980 chunk 525 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 461 GLN A 884 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 410 ASN B 503 ASN B 650 ASN C 6 GLN C 51 GLN C 217 GLN C 260 GLN C 265 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN F 49 GLN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN I 91 HIS L 23 HIS ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 ASN ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 GLN R 194 HIS ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN ** V 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 232 ASN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN c 270 ASN ** c 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 359 GLN d 37 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.104 50489 Z= 0.246 Angle : 0.651 11.664 68726 Z= 0.343 Chirality : 0.044 0.209 7610 Planarity : 0.005 0.067 8447 Dihedral : 15.898 144.019 7649 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 5715 helix: 1.19 (0.11), residues: 2252 sheet: 0.37 (0.18), residues: 832 loop : -0.32 (0.12), residues: 2631 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 601 time to evaluate : 5.805 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 outliers start: 119 outliers final: 35 residues processed: 671 average time/residue: 1.5169 time to fit residues: 1294.8023 Evaluate side-chains 515 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 480 time to evaluate : 6.100 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 25 residues processed: 13 average time/residue: 0.7647 time to fit residues: 23.2425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 292 optimal weight: 9.9990 chunk 163 optimal weight: 0.0170 chunk 437 optimal weight: 0.5980 chunk 358 optimal weight: 0.0970 chunk 145 optimal weight: 0.9980 chunk 526 optimal weight: 50.0000 chunk 569 optimal weight: 30.0000 chunk 469 optimal weight: 10.0000 chunk 522 optimal weight: 8.9990 chunk 179 optimal weight: 0.7980 chunk 422 optimal weight: 9.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 884 ASN A1078 GLN A1163 HIS ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 188 ASN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 GLN C 6 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 GLN ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 343 HIS ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 ASN a 223 HIS b 237 GLN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 50489 Z= 0.197 Angle : 0.603 10.758 68726 Z= 0.314 Chirality : 0.042 0.165 7610 Planarity : 0.004 0.061 8447 Dihedral : 15.738 137.855 7649 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % 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: 0.61 (0.11), residues: 5715 helix: 1.31 (0.11), residues: 2258 sheet: 0.47 (0.18), residues: 834 loop : -0.36 (0.12), residues: 2623 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 548 time to evaluate : 6.064 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 outliers start: 111 outliers final: 47 residues processed: 620 average time/residue: 1.4576 time to fit residues: 1158.5524 Evaluate side-chains 507 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 460 time to evaluate : 5.597 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 33 residues processed: 15 average time/residue: 0.6606 time to fit residues: 23.4975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 520 optimal weight: 50.0000 chunk 396 optimal weight: 3.9990 chunk 273 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 251 optimal weight: 40.0000 chunk 353 optimal weight: 7.9990 chunk 528 optimal weight: 20.0000 chunk 559 optimal weight: 9.9990 chunk 276 optimal weight: 1.9990 chunk 501 optimal weight: 50.0000 chunk 150 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN A 804 HIS A 884 ASN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS C 268 GLN D 38 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN G 14 HIS H 29 HIS ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 GLN ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 ASN ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 223 HIS b 237 GLN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 50489 Z= 0.404 Angle : 0.671 16.300 68726 Z= 0.347 Chirality : 0.045 0.190 7610 Planarity : 0.005 0.061 8447 Dihedral : 15.704 138.462 7649 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % 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: 0.52 (0.11), residues: 5715 helix: 1.22 (0.11), residues: 2251 sheet: 0.38 (0.18), residues: 827 loop : -0.37 (0.12), residues: 2637 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 514 time to evaluate : 6.059 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 outliers start: 140 outliers final: 63 residues processed: 604 average time/residue: 1.4880 time to fit residues: 1162.5738 Evaluate side-chains 502 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 439 time to evaluate : 5.620 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 48 residues processed: 17 average time/residue: 0.6096 time to fit residues: 25.2628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 466 optimal weight: 10.0000 chunk 317 optimal weight: 0.9980 chunk 8 optimal weight: 50.0000 chunk 416 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 477 optimal weight: 8.9990 chunk 386 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 chunk 502 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 723 ASN A 905 ASN A1146 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN E 210 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 287 GLN ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 223 HIS b 210 GLN ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.073 50489 Z= 0.466 Angle : 0.689 14.286 68726 Z= 0.355 Chirality : 0.046 0.287 7610 Planarity : 0.005 0.058 8447 Dihedral : 15.667 140.081 7649 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.11), residues: 5715 helix: 1.15 (0.11), residues: 2237 sheet: 0.20 (0.18), residues: 826 loop : -0.42 (0.12), residues: 2652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 472 time to evaluate : 6.184 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 outliers start: 156 outliers final: 77 residues processed: 589 average time/residue: 1.4741 time to fit residues: 1121.6215 Evaluate side-chains 500 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 423 time to evaluate : 5.783 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 64 residues processed: 16 average time/residue: 0.8725 time to fit residues: 28.8224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 188 optimal weight: 0.9980 chunk 504 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 328 optimal weight: 50.0000 chunk 138 optimal weight: 9.9990 chunk 560 optimal weight: 40.0000 chunk 465 optimal weight: 30.0000 chunk 259 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 620 HIS ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN L 23 HIS ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 327 ASN R 194 HIS a 223 HIS a 232 ASN b 195 HIS ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.096 50489 Z= 0.657 Angle : 0.774 14.981 68726 Z= 0.396 Chirality : 0.049 0.378 7610 Planarity : 0.005 0.078 8447 Dihedral : 15.677 141.824 7649 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 5715 helix: 1.00 (0.11), residues: 2250 sheet: -0.01 (0.17), residues: 843 loop : -0.57 (0.12), residues: 2622 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 468 time to evaluate : 5.673 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 outliers start: 164 outliers final: 95 residues processed: 587 average time/residue: 1.4507 time to fit residues: 1102.1060 Evaluate side-chains 510 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 415 time to evaluate : 5.745 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 78 residues processed: 20 average time/residue: 0.8450 time to fit residues: 33.4670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 540 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 319 optimal weight: 20.0000 chunk 409 optimal weight: 5.9990 chunk 316 optimal weight: 0.9980 chunk 471 optimal weight: 6.9990 chunk 312 optimal weight: 0.6980 chunk 558 optimal weight: 6.9990 chunk 349 optimal weight: 0.7980 chunk 340 optimal weight: 0.8980 chunk 257 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 GLN A1093 GLN ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN D 55 GLN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 89 ASN L 26 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 223 HIS ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 268 ASN ** c 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 312 HIS c 318 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 50489 Z= 0.223 Angle : 0.663 15.313 68726 Z= 0.337 Chirality : 0.043 0.267 7610 Planarity : 0.004 0.052 8447 Dihedral : 15.562 143.950 7649 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.11), residues: 5715 helix: 1.27 (0.11), residues: 2231 sheet: 0.03 (0.17), residues: 834 loop : -0.45 (0.12), residues: 2650 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 442 time to evaluate : 6.138 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 outliers start: 139 outliers final: 86 residues processed: 547 average time/residue: 1.4909 time to fit residues: 1062.3690 Evaluate side-chains 491 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 405 time to evaluate : 5.642 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 75 residues processed: 15 average time/residue: 0.8819 time to fit residues: 27.5730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 345 optimal weight: 0.9990 chunk 222 optimal weight: 0.9980 chunk 333 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 354 optimal weight: 8.9990 chunk 380 optimal weight: 0.4980 chunk 275 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 438 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 GLN ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 50489 Z= 0.315 Angle : 0.685 16.487 68726 Z= 0.347 Chirality : 0.044 0.352 7610 Planarity : 0.004 0.055 8447 Dihedral : 15.504 144.381 7649 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.11), residues: 5715 helix: 1.27 (0.11), residues: 2240 sheet: 0.03 (0.18), residues: 808 loop : -0.47 (0.12), residues: 2667 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 430 time to evaluate : 6.037 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 outliers start: 125 outliers final: 90 residues processed: 526 average time/residue: 1.4989 time to fit residues: 1038.2207 Evaluate side-chains 492 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 402 time to evaluate : 6.263 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 76 residues processed: 16 average time/residue: 1.0196 time to fit residues: 33.2021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 507 optimal weight: 7.9990 chunk 534 optimal weight: 30.0000 chunk 487 optimal weight: 30.0000 chunk 520 optimal weight: 0.0370 chunk 313 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 408 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 469 optimal weight: 10.0000 chunk 491 optimal weight: 40.0000 chunk 518 optimal weight: 10.0000 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 50489 Z= 0.470 Angle : 0.742 15.726 68726 Z= 0.374 Chirality : 0.046 0.328 7610 Planarity : 0.005 0.061 8447 Dihedral : 15.535 144.363 7649 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.11), residues: 5715 helix: 1.17 (0.11), residues: 2237 sheet: -0.04 (0.18), residues: 805 loop : -0.51 (0.12), residues: 2673 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 428 time to evaluate : 5.533 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 outliers start: 118 outliers final: 87 residues processed: 521 average time/residue: 1.4842 time to fit residues: 999.0963 Evaluate side-chains 490 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 403 time to evaluate : 5.614 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 73 residues processed: 16 average time/residue: 0.7633 time to fit residues: 26.5729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 341 optimal weight: 2.9990 chunk 549 optimal weight: 7.9990 chunk 335 optimal weight: 0.3980 chunk 260 optimal weight: 0.9980 chunk 382 optimal weight: 0.0870 chunk 576 optimal weight: 7.9990 chunk 530 optimal weight: 8.9990 chunk 459 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 354 optimal weight: 4.9990 chunk 281 optimal weight: 40.0000 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 50489 Z= 0.239 Angle : 0.718 17.014 68726 Z= 0.359 Chirality : 0.044 0.309 7610 Planarity : 0.004 0.055 8447 Dihedral : 15.464 144.720 7649 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.41 (0.11), residues: 5715 helix: 1.32 (0.11), residues: 2228 sheet: -0.09 (0.17), residues: 827 loop : -0.45 (0.12), residues: 2660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11430 Ramachandran restraints generated. 5715 Oldfield, 0 Emsley, 5715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 438 time to evaluate : 5.777 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 outliers start: 93 outliers final: 74 residues processed: 523 average time/residue: 1.4678 time to fit residues: 997.3373 Evaluate side-chains 486 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 412 time to evaluate : 5.907 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 70 residues processed: 5 average time/residue: 0.9245 time to fit residues: 14.7885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 364 optimal weight: 3.9990 chunk 489 optimal weight: 30.0000 chunk 140 optimal weight: 0.6980 chunk 423 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 460 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 472 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 136 HIS ** a 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.158470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.102501 restraints weight = 105746.679| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.50 r_work: 0.2869 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 50489 Z= 0.273 Angle : 0.722 16.423 68726 Z= 0.361 Chirality : 0.044 0.314 7610 Planarity : 0.004 0.054 8447 Dihedral : 15.426 144.433 7649 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.41 (0.11), residues: 5715 helix: 1.30 (0.11), residues: 2240 sheet: -0.04 (0.18), residues: 817 loop : -0.45 (0.12), residues: 2658 =============================================================================== Job complete usr+sys time: 18534.95 seconds wall clock time: 328 minutes 27.64 seconds (19707.64 seconds total)