Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 14 07:40:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qws_14193/07_2023/7qws_14193_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qws_14193/07_2023/7qws_14193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qws_14193/07_2023/7qws_14193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qws_14193/07_2023/7qws_14193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qws_14193/07_2023/7qws_14193_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qws_14193/07_2023/7qws_14193_neut.pdb" } resolution = 3.4 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= -0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3766 5.49 5 Mg 97 5.21 5 S 251 5.16 5 C 72016 2.51 5 N 25886 2.21 5 O 35892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "t PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 137913 Number of models: 1 Model: "" Number of chains: 55 Chain: "s" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "t" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 531 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "u" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1868 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3148 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "c" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2386 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "e" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "G" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1934 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "i" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "I" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1655 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1703 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "l" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "m" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "N" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "n" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 222 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "O" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "o" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "P" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "Q" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1506 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "r" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "S" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1454 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "T" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "U" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 859 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "V" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "5" Number of atoms: 74854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3493, 74854 Classifications: {'RNA': 3493} Modifications used: {'5*END': 1, 'rna2p_pur': 329, 'rna2p_pyr': 221, 'rna3p_pur': 1575, 'rna3p_pyr': 1367} Link IDs: {'rna2p': 550, 'rna3p': 2942} Chain breaks: 15 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 976 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "7" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "8" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 67} Link IDs: {'rna2p': 26, 'rna3p': 129} Chain: "K" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3337 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Unusual residues: {' MG': 97} Classifications: {'undetermined': 97} Link IDs: {None: 96} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20065 SG CYS g 46 96.872 168.565 198.180 1.00 45.31 S ATOM 20082 SG CYS g 49 96.324 172.308 197.275 1.00 49.92 S ATOM 20345 SG CYS g 83 98.373 171.453 200.275 1.00 42.81 S ATOM 20365 SG CYS g 86 94.684 170.708 200.322 1.00 49.19 S ATOM 27693 SG CYS j 19 125.122 122.591 176.903 1.00 25.78 S ATOM 27721 SG CYS j 22 126.629 120.570 174.052 1.00 25.01 S ATOM 27812 SG CYS j 34 123.229 122.181 173.657 1.00 23.64 S ATOM 27831 SG CYS j 37 123.654 119.159 175.900 1.00 24.12 S ATOM 33626 SG CYS m 96 108.483 140.387 64.127 1.00 34.63 S ATOM 33652 SG CYS m 99 111.742 141.451 65.792 1.00 32.96 S ATOM 33742 SG CYS m 110 111.897 140.004 62.372 1.00 36.80 S ATOM 33786 SG CYS m 115 110.995 137.744 65.250 1.00 31.99 S ATOM 37545 SG CYS o 12 60.074 68.411 134.351 1.00 41.63 S ATOM 37569 SG CYS o 15 57.412 65.704 134.496 1.00 45.35 S ATOM 38038 SG CYS o 72 56.455 69.368 135.100 1.00 45.25 S ATOM 38075 SG CYS o 77 58.439 67.391 137.662 1.00 55.09 S ATOM 39847 SG CYS p 39 84.370 174.134 187.984 1.00 35.25 S ATOM 39870 SG CYS p 42 85.855 177.613 188.366 1.00 38.58 S ATOM 39992 SG CYS p 57 88.075 174.673 187.408 1.00 32.88 S ATOM 40008 SG CYS p 60 86.674 175.096 190.956 1.00 38.74 S Time building chain proxies: 47.37, per 1000 atoms: 0.34 Number of scatterers: 137913 At special positions: 0 Unit cell: (235.664, 247.715, 274.495, 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 5 29.99 S 251 16.00 P 3766 15.00 Mg 97 11.99 O 35892 8.00 N 25886 7.00 C 72016 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: 53.73 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 110 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 99 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 115 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 96 " pdb=" ZN o 201 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 72 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " Number of angles added : 30 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13192 Finding SS restraints... Secondary structure from input PDB file: 249 helices and 75 sheets defined 39.8% alpha, 14.6% beta 1168 base pairs and 1779 stacking pairs defined. Time for finding SS restraints: 40.85 Creating SS restraints... Processing helix chain 't' and resid 70 through 84 removed outlier: 3.764A pdb=" N LEU t 83 " --> pdb=" O ALA t 79 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY t 84 " --> pdb=" O MET t 80 " (cutoff:3.500A) Processing helix chain 'u' and resid 7 through 19 removed outlier: 3.681A pdb=" N ARG u 19 " --> pdb=" O GLN u 15 " (cutoff:3.500A) Processing helix chain 'u' and resid 39 through 50 removed outlier: 4.232A pdb=" N LYS u 43 " --> pdb=" O ALA u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 100 through 110 removed outlier: 4.025A pdb=" N LEU u 103 " --> pdb=" O THR u 100 " (cutoff:3.500A) Proline residue: u 104 - end of helix removed outlier: 5.569A pdb=" N LEU u 107 " --> pdb=" O PRO u 104 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASN u 108 " --> pdb=" O SER u 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.570A pdb=" N ARG A 17 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.750A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'b' and resid 11 through 19 removed outlier: 4.146A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 49 Processing helix chain 'b' and resid 50 through 52 No H-bonds generated for 'chain 'b' and resid 50 through 52' Processing helix chain 'b' and resid 53 through 76 Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 139 through 157 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.665A pdb=" N ARG B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.378A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'c' and resid 14 through 24 Processing helix chain 'c' and resid 30 through 40 Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 85 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 116 through 132 removed outlier: 3.767A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.818A pdb=" N VAL C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.710A pdb=" N LYS C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 removed outlier: 4.347A pdb=" N ASN C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 removed outlier: 3.585A pdb=" N HIS C 245 " --> pdb=" O PRO C 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 245' Processing helix chain 'C' and resid 254 through 264 removed outlier: 3.695A pdb=" N LEU C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.741A pdb=" N ILE C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 321 through 329 removed outlier: 3.891A pdb=" N MET C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 338 removed outlier: 4.324A pdb=" N THR C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 363 Processing helix chain 'd' and resid 29 through 33 Processing helix chain 'd' and resid 37 through 39 No H-bonds generated for 'chain 'd' and resid 37 through 39' Processing helix chain 'd' and resid 40 through 57 removed outlier: 3.527A pdb=" N MET d 57 " --> pdb=" O ALA d 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.955A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 94 through 113 Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 201 through 215 removed outlier: 4.081A pdb=" N ALA D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 Processing helix chain 'D' and resid 223 through 228 removed outlier: 3.585A pdb=" N ILE D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 223 through 228' Processing helix chain 'D' and resid 232 through 250 removed outlier: 4.188A pdb=" N GLU D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 292 Processing helix chain 'e' and resid 57 through 61 Processing helix chain 'e' and resid 81 through 86 Processing helix chain 'e' and resid 87 through 90 removed outlier: 4.309A pdb=" N MET e 90 " --> pdb=" O VAL e 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 87 through 90' Processing helix chain 'e' and resid 104 through 118 removed outlier: 3.809A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 128 through 132 Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 209 through 213 Processing helix chain 'E' and resid 239 through 260 removed outlier: 3.863A pdb=" N LYS E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix removed outlier: 4.227A pdb=" N VAL E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 269 Processing helix chain 'f' and resid 37 through 43 removed outlier: 4.101A pdb=" N GLU f 40 " --> pdb=" O ASP f 37 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE f 41 " --> pdb=" O GLU f 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 80 removed outlier: 4.005A pdb=" N ALA F 80 " --> pdb=" O MET F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 114 Processing helix chain 'F' and resid 128 through 138 removed outlier: 3.630A pdb=" N VAL F 138 " --> pdb=" O MET F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 159 Processing helix chain 'F' and resid 173 through 182 removed outlier: 4.187A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 198 Processing helix chain 'F' and resid 202 through 210 Processing helix chain 'F' and resid 241 through 250 Processing helix chain 'g' and resid 60 through 66 removed outlier: 3.632A pdb=" N MET g 65 " --> pdb=" O LYS g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 73 removed outlier: 4.113A pdb=" N HIS g 73 " --> pdb=" O THR g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 115 Processing helix chain 'G' and resid 58 through 74 Processing helix chain 'G' and resid 77 through 82 Processing helix chain 'G' and resid 88 through 101 removed outlier: 3.666A pdb=" N GLN G 94 " --> pdb=" O GLN G 90 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 120 removed outlier: 3.531A pdb=" N LYS G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 169 through 178 Processing helix chain 'G' and resid 186 through 194 removed outlier: 3.676A pdb=" N LEU G 190 " --> pdb=" O GLY G 186 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 224 removed outlier: 3.688A pdb=" N THR G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 235 Processing helix chain 'G' and resid 243 through 261 removed outlier: 3.664A pdb=" N LEU G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 12 removed outlier: 3.960A pdb=" N GLY h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 37 Processing helix chain 'h' and resid 40 through 73 removed outlier: 3.813A pdb=" N ILE h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 88 through 93 Processing helix chain 'h' and resid 104 through 114 Processing helix chain 'H' and resid 49 through 52 Processing helix chain 'H' and resid 63 through 86 removed outlier: 3.828A pdb=" N ALA H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.691A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 30 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 63 removed outlier: 3.633A pdb=" N VAL i 63 " --> pdb=" O GLU i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 77 Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.721A pdb=" N ALA i 102 " --> pdb=" O ARG i 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 10 removed outlier: 3.970A pdb=" N ARG I 10 " --> pdb=" O ARG I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 80 Processing helix chain 'I' and resid 144 through 157 Processing helix chain 'I' and resid 177 through 187 removed outlier: 4.103A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 212 removed outlier: 3.899A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 9 removed outlier: 3.797A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 57 removed outlier: 3.744A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 75 removed outlier: 4.060A pdb=" N ARG j 75 " --> pdb=" O TYR j 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 14 removed outlier: 4.080A pdb=" N ARG J 13 " --> pdb=" O ASN J 10 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU J 14 " --> pdb=" O PRO J 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 10 through 14' Processing helix chain 'J' and resid 30 through 45 removed outlier: 3.589A pdb=" N ALA J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 112 through 116 Processing helix chain 'J' and resid 138 through 143 removed outlier: 3.899A pdb=" N ILE J 141 " --> pdb=" O GLY J 138 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 142 " --> pdb=" O PHE J 139 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP J 143 " --> pdb=" O SER J 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 138 through 143' Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'k' and resid 7 through 16 removed outlier: 3.918A pdb=" N PHE k 11 " --> pdb=" O GLU k 7 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 58 removed outlier: 3.664A pdb=" N ALA k 53 " --> pdb=" O ASP k 49 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 62 through 67 removed outlier: 4.705A pdb=" N TYR L 66 " --> pdb=" O PRO L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 87 through 95 removed outlier: 4.133A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 123 Processing helix chain 'L' and resid 139 through 143 Processing helix chain 'L' and resid 170 through 175 removed outlier: 3.668A pdb=" N LYS L 174 " --> pdb=" O THR L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 211 removed outlier: 5.442A pdb=" N GLY L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE L 194 " --> pdb=" O ARG L 190 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 20 Processing helix chain 'l' and resid 24 through 30 removed outlier: 3.537A pdb=" N ILE l 27 " --> pdb=" O PRO l 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 81 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 89 through 103 Processing helix chain 'M' and resid 105 through 139 removed outlier: 3.766A pdb=" N MET M 118 " --> pdb=" O LYS M 114 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 91 removed outlier: 3.511A pdb=" N LYS m 88 " --> pdb=" O GLN m 84 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.748A pdb=" N LEU N 33 " --> pdb=" O GLN N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 50 Processing helix chain 'N' and resid 83 through 88 removed outlier: 4.404A pdb=" N GLY N 88 " --> pdb=" O VAL N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 145 through 157 removed outlier: 3.741A pdb=" N GLN N 149 " --> pdb=" O PRO N 146 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TRP N 150 " --> pdb=" O ASP N 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE N 151 " --> pdb=" O THR N 148 " (cutoff:3.500A) Proline residue: N 154 - end of helix removed outlier: 3.684A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 removed outlier: 3.502A pdb=" N SER N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 196 Processing helix chain 'n' and resid 3 through 24 removed outlier: 3.560A pdb=" N SER n 24 " --> pdb=" O MET n 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 29 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 60 Processing helix chain 'O' and resid 65 through 69 Processing helix chain 'O' and resid 75 through 87 Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 109 through 114 removed outlier: 4.303A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 185 removed outlier: 3.601A pdb=" N THR O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL O 185 " --> pdb=" O ALA O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 199 removed outlier: 3.973A pdb=" N VAL O 195 " --> pdb=" O ARG O 191 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU O 196 " --> pdb=" O PHE O 192 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS O 199 " --> pdb=" O VAL O 195 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 46 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 54 through 66 Processing helix chain 'P' and resid 69 through 82 Processing helix chain 'P' and resid 99 through 106 Processing helix chain 'P' and resid 113 through 135 Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'P' and resid 161 through 163 No H-bonds generated for 'chain 'P' and resid 161 through 163' Processing helix chain 'p' and resid 8 through 15 removed outlier: 3.797A pdb=" N VAL p 11 " --> pdb=" O VAL p 8 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 34 removed outlier: 4.159A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 removed outlier: 3.819A pdb=" N GLN p 92 " --> pdb=" O GLU p 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 53 removed outlier: 4.263A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 70 Processing helix chain 'Q' and resid 106 through 116 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 142 through 152 removed outlier: 4.261A pdb=" N ARG Q 146 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU Q 147 " --> pdb=" O LYS Q 144 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL Q 148 " --> pdb=" O GLY Q 145 " (cutoff:3.500A) Processing helix chain 'r' and resid 3 through 11 Processing helix chain 'r' and resid 87 through 99 Processing helix chain 'r' and resid 103 through 105 No H-bonds generated for 'chain 'r' and resid 103 through 105' Processing helix chain 'r' and resid 106 through 121 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 25 through 27 No H-bonds generated for 'chain 'R' and resid 25 through 27' Processing helix chain 'R' and resid 28 through 34 Processing helix chain 'R' and resid 40 through 48 Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 81 removed outlier: 3.641A pdb=" N LYS R 80 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG R 81 " --> pdb=" O ILE R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 81' Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 134 through 181 removed outlier: 3.882A pdb=" N LEU R 138 " --> pdb=" O ASN R 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 101 through 118 Processing helix chain 'S' and resid 120 through 122 No H-bonds generated for 'chain 'S' and resid 120 through 122' Processing helix chain 'S' and resid 139 through 144 Processing helix chain 'T' and resid 26 through 30 removed outlier: 3.741A pdb=" N THR T 29 " --> pdb=" O PRO T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 58 removed outlier: 3.591A pdb=" N HIS T 58 " --> pdb=" O LYS T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 118 removed outlier: 3.611A pdb=" N PHE T 105 " --> pdb=" O SER T 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 32 Processing helix chain 'U' and resid 35 through 47 Processing helix chain 'U' and resid 53 through 58 removed outlier: 3.844A pdb=" N LEU U 56 " --> pdb=" O ALA U 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY U 57 " --> pdb=" O GLY U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 94 removed outlier: 4.201A pdb=" N LEU U 83 " --> pdb=" O SER U 79 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 73 Processing helix chain 'V' and resid 122 through 129 Processing helix chain 'V' and resid 129 through 136 Processing helix chain 'W' and resid 33 through 42 Processing helix chain 'W' and resid 52 through 60 removed outlier: 3.537A pdb=" N ARG W 56 " --> pdb=" O THR W 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 76 Processing helix chain 'X' and resid 83 through 92 removed outlier: 3.696A pdb=" N LYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS X 89 " --> pdb=" O SER X 85 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE X 90 " --> pdb=" O ALA X 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU X 91 " --> pdb=" O MET X 87 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 118 removed outlier: 3.590A pdb=" N LYS X 115 " --> pdb=" O GLN X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 152 removed outlier: 4.158A pdb=" N LYS X 152 " --> pdb=" O ASP X 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 3.990A pdb=" N LYS Y 28 " --> pdb=" O HIS Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 134 removed outlier: 3.533A pdb=" N LYS Y 117 " --> pdb=" O LYS Y 113 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE Y 118 " --> pdb=" O ASP Y 114 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG Y 126 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY Y 133 " --> pdb=" O GLY Y 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 78 removed outlier: 4.112A pdb=" N LEU K 68 " --> pdb=" O LYS K 64 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP K 70 " --> pdb=" O GLN K 66 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR K 73 " --> pdb=" O VAL K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 83 removed outlier: 4.064A pdb=" N THR K 82 " --> pdb=" O CYS K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 88 Processing helix chain 'K' and resid 90 through 111 removed outlier: 3.522A pdb=" N GLN K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL K 109 " --> pdb=" O GLN K 105 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL K 110 " --> pdb=" O MET K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 126 Processing helix chain 'K' and resid 127 through 129 No H-bonds generated for 'chain 'K' and resid 127 through 129' Processing helix chain 'K' and resid 134 through 148 removed outlier: 3.653A pdb=" N LYS K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA K 144 " --> pdb=" O LEU K 140 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL K 145 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS K 146 " --> pdb=" O SER K 142 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 147 " --> pdb=" O LYS K 143 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU K 148 " --> pdb=" O ALA K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 removed outlier: 4.005A pdb=" N GLY K 166 " --> pdb=" O TYR K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 182 removed outlier: 4.015A pdb=" N ALA K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR K 173 " --> pdb=" O ALA K 169 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS K 174 " --> pdb=" O ALA K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 197 removed outlier: 3.920A pdb=" N SER K 192 " --> pdb=" O LEU K 188 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET K 193 " --> pdb=" O GLN K 189 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL K 194 " --> pdb=" O ASN K 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN K 197 " --> pdb=" O MET K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 224 removed outlier: 3.607A pdb=" N VAL K 210 " --> pdb=" O HIS K 206 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET K 211 " --> pdb=" O SER K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 245 removed outlier: 3.932A pdb=" N TRP K 231 " --> pdb=" O ASP K 227 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER K 244 " --> pdb=" O SER K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 266 removed outlier: 3.769A pdb=" N SER K 252 " --> pdb=" O ASN K 248 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN K 253 " --> pdb=" O PRO K 249 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA K 260 " --> pdb=" O LEU K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 285 removed outlier: 3.983A pdb=" N HIS K 276 " --> pdb=" O ASN K 272 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR K 285 " --> pdb=" O THR K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 303 removed outlier: 4.035A pdb=" N GLU K 294 " --> pdb=" O GLY K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 329 removed outlier: 4.209A pdb=" N ARG K 310 " --> pdb=" O TRP K 306 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU K 313 " --> pdb=" O PRO K 309 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU K 327 " --> pdb=" O LEU K 323 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU K 328 " --> pdb=" O THR K 324 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER K 329 " --> pdb=" O SER K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 343 Processing helix chain 'K' and resid 346 through 354 Proline residue: K 352 - end of helix Processing helix chain 'K' and resid 372 through 376 removed outlier: 3.513A pdb=" N LEU K 376 " --> pdb=" O LEU K 373 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 464 Processing helix chain 'K' and resid 473 through 477 Processing helix chain 'Z' and resid 59 through 66 removed outlier: 3.667A pdb=" N ALA Z 63 " --> pdb=" O LYS Z 59 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 97 through 101 removed outlier: 3.956A pdb=" N PHE Z 101 " --> pdb=" O LYS Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 123 removed outlier: 3.740A pdb=" N GLU Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS Z 117 " --> pdb=" O GLU Z 113 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE Z 118 " --> pdb=" O ALA Z 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 removed outlier: 4.123A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 5 Processing helix chain 'a' and resid 6 through 11 removed outlier: 4.046A pdb=" N LYS a 10 " --> pdb=" O ARG a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 76 through 82 removed outlier: 4.961A pdb=" N TRP a 79 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU a 81 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL a 82 " --> pdb=" O TRP a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 90 removed outlier: 3.852A pdb=" N ARG a 87 " --> pdb=" O SER a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 141 Processing sheet with id=AA1, first strand: chain 't' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 't' and resid 127 through 130 removed outlier: 3.570A pdb=" N ILE t 102 " --> pdb=" O LYS t 98 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG t 93 " --> pdb=" O PHE u 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU u 61 " --> pdb=" O ARG t 97 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR u 70 " --> pdb=" O THR u 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 77 removed outlier: 4.062A pdb=" N ASP A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 62 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL A 45 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ARG A 64 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLY A 43 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.727A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N HIS A 139 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS A 145 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.646A pdb=" N HIS B 42 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 186 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 159 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N HIS B 165 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL B 86 " --> pdb=" O HIS B 165 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL B 93 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N THR B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.646A pdb=" N HIS B 42 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 186 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 159 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N HIS B 165 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL B 86 " --> pdb=" O HIS B 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 365 through 368 removed outlier: 6.559A pdb=" N VAL B 57 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE B 368 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS B 55 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 219 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ILE B 280 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLY B 221 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR B 278 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS B 283 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET B 332 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 333 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 52 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AB1, first strand: chain 'B' and resid 292 through 293 removed outlier: 4.334A pdb=" N LEU B 292 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.769A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL c 46 " --> pdb=" O HIS c 72 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR c 74 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU c 48 " --> pdb=" O TYR c 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 7 through 9 Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.182A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 253 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB7, first strand: chain 'd' and resid 21 through 28 removed outlier: 4.179A pdb=" N VAL d 21 " --> pdb=" O ARG d 90 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG d 63 " --> pdb=" O VAL d 106 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N TYR d 108 " --> pdb=" O ARG d 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 73 through 79 removed outlier: 5.649A pdb=" N ILE D 74 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TYR D 66 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS D 76 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET D 51 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 142 through 143 removed outlier: 5.799A pdb=" N PHE D 142 " --> pdb=" O SER D 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 183 through 184 removed outlier: 3.651A pdb=" N GLU D 189 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 75 through 79 Processing sheet with id=AC3, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.832A pdb=" N LYS E 156 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N THR E 195 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE E 147 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR E 193 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AC5, first strand: chain 'f' and resid 7 through 16 removed outlier: 5.315A pdb=" N PHE f 11 " --> pdb=" O LYS f 29 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS f 29 " --> pdb=" O PHE f 11 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY f 13 " --> pdb=" O LEU f 27 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR f 25 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS f 24 " --> pdb=" O PHE f 88 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE f 88 " --> pdb=" O HIS f 24 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET f 83 " --> pdb=" O ALA f 77 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA f 77 " --> pdb=" O MET f 83 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG f 85 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR f 67 " --> pdb=" O ASN f 55 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ASN f 55 " --> pdb=" O THR f 67 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N VAL f 69 " --> pdb=" O ALA f 53 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ALA f 53 " --> pdb=" O VAL f 69 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N TRP f 71 " --> pdb=" O TYR f 51 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N TYR f 51 " --> pdb=" O TRP f 71 " (cutoff:3.500A) removed outlier: 11.021A pdb=" N LYS f 73 " --> pdb=" O TYR f 49 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N TYR f 49 " --> pdb=" O LYS f 73 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N THR f 75 " --> pdb=" O CYS f 47 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N CYS f 47 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL f 50 " --> pdb=" O ARG f 100 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ARG f 100 " --> pdb=" O VAL f 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 82 through 85 removed outlier: 3.638A pdb=" N PHE F 83 " --> pdb=" O VAL T 141 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS T 139 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 213 through 214 removed outlier: 4.004A pdb=" N ASN F 121 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE F 142 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ARG F 238 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP F 144 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 161 through 164 Processing sheet with id=AC9, first strand: chain 'g' and resid 20 through 24 removed outlier: 3.637A pdb=" N SER g 23 " --> pdb=" O VAL g 31 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 181 through 184 removed outlier: 6.305A pdb=" N VAL G 155 " --> pdb=" O CYS G 182 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE G 157 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 154 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'h' and resid 119 through 121 Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 11 removed outlier: 7.365A pdb=" N ILE H 4 " --> pdb=" O TRP H 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP H 61 " --> pdb=" O ILE H 4 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 17 through 21 removed outlier: 3.512A pdb=" N LYS H 21 " --> pdb=" O THR H 24 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 24 " --> pdb=" O LYS H 21 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 133 through 136 removed outlier: 6.699A pdb=" N ARG H 89 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS H 184 " --> pdb=" O ARG H 89 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS H 91 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 102 through 105 removed outlier: 3.900A pdb=" N ASN H 102 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG H 115 " --> pdb=" O ASN H 102 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 35 through 37 removed outlier: 6.744A pdb=" N MET I 52 " --> pdb=" O ILE I 135 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER I 137 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY I 50 " --> pdb=" O SER I 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 58 through 61 removed outlier: 5.714A pdb=" N ILE I 99 " --> pdb=" O PRO I 122 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY I 124 " --> pdb=" O ILE I 97 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 190 through 193 removed outlier: 3.644A pdb=" N ILE I 191 " --> pdb=" O LYS I 198 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'j' and resid 16 through 18 Processing sheet with id=AE2, first strand: chain 'J' and resid 49 through 51 removed outlier: 3.591A pdb=" N ALA J 69 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE J 17 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY J 135 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS J 19 " --> pdb=" O VAL J 133 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN J 23 " --> pdb=" O ASP J 129 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP J 129 " --> pdb=" O ASN J 23 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'k' and resid 4 through 5 removed outlier: 4.355A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 22 through 24 Processing sheet with id=AE5, first strand: chain 'L' and resid 59 through 60 Processing sheet with id=AE6, first strand: chain 'M' and resid 7 through 8 removed outlier: 3.538A pdb=" N PHE S 152 " --> pdb=" O VAL M 7 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 45 through 51 removed outlier: 4.928A pdb=" N ARG M 46 " --> pdb=" O GLY M 40 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLY M 40 " --> pdb=" O ARG M 46 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG M 35 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP M 29 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP M 39 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE M 27 " --> pdb=" O ASP M 39 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL M 12 " --> pdb=" O THR M 58 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'm' and resid 102 through 103 Processing sheet with id=AE9, first strand: chain 'N' and resid 36 through 39 removed outlier: 3.507A pdb=" N HIS N 37 " --> pdb=" O ARG N 63 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N TYR N 127 " --> pdb=" O GLY N 122 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLY N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TRP N 120 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 7 through 10 removed outlier: 6.069A pdb=" N LEU O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL O 36 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL O 33 " --> pdb=" O LYS O 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AF3, first strand: chain 'o' and resid 3 through 4 Processing sheet with id=AF4, first strand: chain 'o' and resid 7 through 11 Processing sheet with id=AF5, first strand: chain 'P' and resid 43 through 51 removed outlier: 3.783A pdb=" N ASN P 50 " --> pdb=" O CYS P 173 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS P 173 " --> pdb=" O ASN P 50 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR P 180 " --> pdb=" O ILE P 143 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE P 143 " --> pdb=" O THR P 180 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 157 through 160 removed outlier: 3.755A pdb=" N ARG P 164 " --> pdb=" O ARG P 160 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'p' and resid 37 through 38 removed outlier: 6.709A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.374A pdb=" N LEU Q 61 " --> pdb=" O THR Q 87 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL Q 82 " --> pdb=" O VAL Q 100 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA Q 102 " --> pdb=" O VAL Q 82 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLY Q 84 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG Q 104 " --> pdb=" O GLY Q 84 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA Q 102 " --> pdb=" O LEU Q 121 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.374A pdb=" N LEU Q 61 " --> pdb=" O THR Q 87 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR Q 79 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'r' and resid 17 through 18 Processing sheet with id=AG2, first strand: chain 'r' and resid 49 through 53 removed outlier: 3.553A pdb=" N VAL r 62 " --> pdb=" O THR r 80 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR r 80 " --> pdb=" O VAL r 62 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 22 through 23 removed outlier: 3.653A pdb=" N ILE R 51 " --> pdb=" O TRP R 23 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 59 through 66 removed outlier: 6.387A pdb=" N VAL S 13 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N CYS S 64 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS S 11 " --> pdb=" O CYS S 64 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN S 66 " --> pdb=" O GLU S 9 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLU S 9 " --> pdb=" O GLN S 66 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 91 through 99 removed outlier: 6.844A pdb=" N ASN S 77 " --> pdb=" O GLU S 131 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU S 131 " --> pdb=" O ASN S 77 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLY S 79 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL S 129 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TRP S 81 " --> pdb=" O MET S 127 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 83 through 92 removed outlier: 6.503A pdb=" N VAL T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL T 64 " --> pdb=" O VAL T 75 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ASN T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY T 62 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'U' and resid 19 through 24 removed outlier: 3.834A pdb=" N THR U 71 " --> pdb=" O GLU U 64 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 100 through 103 removed outlier: 3.524A pdb=" N ARG U 113 " --> pdb=" O ARG U 101 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 25 through 28 removed outlier: 6.881A pdb=" N ASN V 36 " --> pdb=" O LYS V 66 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET V 62 " --> pdb=" O ILE V 40 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL V 42 " --> pdb=" O MET V 60 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N MET V 60 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA V 102 " --> pdb=" O ILE V 82 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLY V 103 " --> pdb=" O VAL V 25 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN V 27 " --> pdb=" O GLY V 103 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE V 105 " --> pdb=" O ASN V 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 88 through 89 removed outlier: 5.837A pdb=" N PHE V 95 " --> pdb=" O ARG W 20 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA W 22 " --> pdb=" O PHE V 95 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR V 97 " --> pdb=" O ALA W 22 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 4 through 5 removed outlier: 3.684A pdb=" N GLU W 4 " --> pdb=" O ILE W 13 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'X' and resid 77 through 80 removed outlier: 3.605A pdb=" N PHE X 79 " --> pdb=" O ILE X 99 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS X 134 " --> pdb=" O VAL X 100 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AH5, first strand: chain 'Y' and resid 79 through 82 removed outlier: 7.519A pdb=" N VAL Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL Y 73 " --> pdb=" O VAL Y 79 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N TYR Y 81 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AH7, first strand: chain 'K' and resid 379 through 380 removed outlier: 4.235A pdb=" N ASN K 439 " --> pdb=" O ARG K 458 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER K 456 " --> pdb=" O ARG K 441 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA K 415 " --> pdb=" O SER K 455 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.572A pdb=" N VAL K 466 " --> pdb=" O ALA K 434 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 393 through 394 removed outlier: 3.572A pdb=" N THR K 403 " --> pdb=" O LEU K 394 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.576A pdb=" N LYS Z 69 " --> pdb=" O ASP Z 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL Z 43 " --> pdb=" O LYS Z 73 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS Z 40 " --> pdb=" O ASN Z 28 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASN Z 28 " --> pdb=" O HIS Z 40 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE Z 46 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'a' and resid 72 through 74 removed outlier: 6.338A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'a' and resid 100 through 102 removed outlier: 6.179A pdb=" N VAL a 124 " --> pdb=" O VAL a 145 " (cutoff:3.500A) 2191 hydrogen bonds defined for protein. 6135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3049 hydrogen bonds 5194 hydrogen bond angles 0 basepair planarities 1168 basepair parallelities 1779 stacking parallelities Total time for adding SS restraints: 208.60 Time building geometry restraints manager: 58.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 21380 1.33 - 1.45: 58285 1.45 - 1.57: 60823 1.57 - 1.70: 7517 1.70 - 1.82: 402 Bond restraints: 148407 Sorted by residual: bond pdb=" C GLY i 49 " pdb=" O GLY i 49 " ideal model delta sigma weight residual 1.236 1.248 -0.012 5.30e-03 3.56e+04 5.20e+00 bond pdb=" C PHE S 78 " pdb=" N GLY S 79 " ideal model delta sigma weight residual 1.332 1.342 -0.010 5.00e-03 4.00e+04 4.22e+00 bond pdb=" C2 C 51566 " pdb=" O2 C 51566 " ideal model delta sigma weight residual 1.240 1.273 -0.033 2.00e-02 2.50e+03 2.80e+00 bond pdb=" CA PRO G 133 " pdb=" C PRO G 133 " ideal model delta sigma weight residual 1.517 1.528 -0.011 6.70e-03 2.23e+04 2.69e+00 bond pdb=" C2 C 51566 " pdb=" N3 C 51566 " ideal model delta sigma weight residual 1.353 1.385 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 148402 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.66: 23475 106.66 - 113.51: 86697 113.51 - 120.35: 54935 120.35 - 127.20: 45124 127.20 - 134.04: 8346 Bond angle restraints: 218577 Sorted by residual: angle pdb=" C3' A 55061 " pdb=" O3' A 55061 " pdb=" P G 55062 " ideal model delta sigma weight residual 120.20 128.15 -7.95 1.50e+00 4.44e-01 2.81e+01 angle pdb=" C2' A 5 334 " pdb=" C1' A 5 334 " pdb=" N9 A 5 334 " ideal model delta sigma weight residual 112.00 118.67 -6.67 1.50e+00 4.44e-01 1.97e+01 angle pdb=" O3' A 55061 " pdb=" C3' A 55061 " pdb=" C2' A 55061 " ideal model delta sigma weight residual 109.50 116.03 -6.53 1.50e+00 4.44e-01 1.90e+01 angle pdb=" O3' C 52083 " pdb=" C3' C 52083 " pdb=" C2' C 52083 " ideal model delta sigma weight residual 109.50 115.99 -6.49 1.50e+00 4.44e-01 1.87e+01 angle pdb=" O3' A 55061 " pdb=" P G 55062 " pdb=" OP2 G 55062 " ideal model delta sigma weight residual 108.00 118.96 -10.96 3.00e+00 1.11e-01 1.33e+01 ... (remaining 218572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 78965 35.99 - 71.98: 2127 71.98 - 107.98: 207 107.98 - 143.97: 28 143.97 - 179.96: 86 Dihedral angle restraints: 81413 sinusoidal: 60956 harmonic: 20457 Sorted by residual: dihedral pdb=" C4' C 52083 " pdb=" C3' C 52083 " pdb=" C2' C 52083 " pdb=" C1' C 52083 " ideal model delta sinusoidal sigma weight residual -35.00 33.23 -68.23 1 8.00e+00 1.56e-02 9.44e+01 dihedral pdb=" C5' C 52083 " pdb=" C4' C 52083 " pdb=" C3' C 52083 " pdb=" O3' C 52083 " ideal model delta sinusoidal sigma weight residual 147.00 79.84 67.16 1 8.00e+00 1.56e-02 9.18e+01 dihedral pdb=" O4' C 54413 " pdb=" C1' C 54413 " pdb=" N1 C 54413 " pdb=" C2 C 54413 " ideal model delta sinusoidal sigma weight residual -160.00 12.70 -172.70 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 81410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 26737 0.097 - 0.193: 454 0.193 - 0.290: 7 0.290 - 0.387: 1 0.387 - 0.484: 1 Chirality restraints: 27200 Sorted by residual: chirality pdb=" C1' A 5 334 " pdb=" O4' A 5 334 " pdb=" C2' A 5 334 " pdb=" N9 A 5 334 " both_signs ideal model delta sigma weight residual False 2.46 1.97 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C3' C 52083 " pdb=" C4' C 52083 " pdb=" O3' C 52083 " pdb=" C2' C 52083 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" P G 55062 " pdb=" OP1 G 55062 " pdb=" OP2 G 55062 " pdb=" O5' G 55062 " both_signs ideal model delta sigma weight residual True 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 27197 not shown) Planarity restraints: 13640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR f 106 " 0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO f 107 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO f 107 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO f 107 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A 5 334 " 0.042 2.00e-02 2.50e+03 2.01e-02 1.11e+01 pdb=" N9 A 5 334 " -0.050 2.00e-02 2.50e+03 pdb=" C8 A 5 334 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A 5 334 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A 5 334 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 5 334 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A 5 334 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A 5 334 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 5 334 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A 5 334 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 5 334 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 52330 " 0.041 2.00e-02 2.50e+03 1.72e-02 8.83e+00 pdb=" N9 G 52330 " -0.038 2.00e-02 2.50e+03 pdb=" C8 G 52330 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G 52330 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 52330 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 52330 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G 52330 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G 52330 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G 52330 " -0.010 2.00e-02 2.50e+03 pdb=" N2 G 52330 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G 52330 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G 52330 " -0.006 2.00e-02 2.50e+03 ... (remaining 13637 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1586 2.59 - 3.17: 107363 3.17 - 3.74: 262663 3.74 - 4.32: 352502 4.32 - 4.90: 501364 Nonbonded interactions: 1225478 Sorted by model distance: nonbonded pdb=" OP1 G 53916 " pdb="MG MG 55111 " model vdw 2.011 2.170 nonbonded pdb=" OP2 G 54650 " pdb="MG MG 55183 " model vdw 2.021 2.170 nonbonded pdb=" O6 G 51321 " pdb="MG MG 55195 " model vdw 2.024 2.170 nonbonded pdb=" OP1 A 53642 " pdb="MG MG 55181 " model vdw 2.029 2.170 nonbonded pdb=" OP2 C 52411 " pdb="MG MG 55115 " model vdw 2.045 2.170 ... (remaining 1225473 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.120 Extract box with map and model: 21.980 Check model and map are aligned: 1.520 Set scattering table: 0.880 Process input model: 465.060 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 498.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 148407 Z= 0.111 Angle : 0.465 10.955 218577 Z= 0.237 Chirality : 0.029 0.484 27200 Planarity : 0.003 0.088 13640 Dihedral : 14.635 179.962 68221 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.67 % Favored : 96.32 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 6953 helix: 1.56 (0.11), residues: 2353 sheet: 0.43 (0.18), residues: 925 loop : -0.53 (0.10), residues: 3675 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 734 time to evaluate : 6.517 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: 100 outliers final: 21 residues processed: 825 average time/residue: 1.3847 time to fit residues: 1903.6449 Evaluate side-chains 435 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 414 time to evaluate : 6.399 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.9608 time to fit residues: 47.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 896 optimal weight: 9.9990 chunk 804 optimal weight: 9.9990 chunk 446 optimal weight: 1.9990 chunk 274 optimal weight: 0.0270 chunk 542 optimal weight: 3.9990 chunk 430 optimal weight: 1.9990 chunk 832 optimal weight: 9.9990 chunk 322 optimal weight: 7.9990 chunk 506 optimal weight: 8.9990 chunk 619 optimal weight: 30.0000 chunk 964 optimal weight: 10.0000 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 63 ASN u 76 ASN u 80 GLN A 22 HIS b 7 HIS b 49 HIS b 50 ASN b 58 GLN b 61 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 186 ASN B 245 HIS B 275 HIS B 289 GLN B 315 ASN B 380 GLN c 19 GLN C 38 ASN C 50 GLN C 142 HIS C 198 ASN C 212 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 329 ASN C 346 ASN d 18 ASN d 93 ASN ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN e 24 GLN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 101 HIS ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS E 217 GLN E 246 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 ASN F 112 GLN g 28 ASN G 100 HIS G 141 ASN G 159 HIS ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 HIS H 162 GLN I 59 GLN I 92 HIS ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 ASN J 42 GLN J 98 ASN k 31 ASN k 58 GLN ** L 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 87 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 149 GLN L 175 ASN l 38 ASN M 20 HIS M 33 GLN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 104 HIS m 119 ASN N 32 GLN N 182 HIS N 196 ASN O 26 GLN O 63 ASN ** O 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 GLN o 21 HIS o 36 GLN o 51 GLN o 102 GLN P 50 ASN P 54 HIS P 57 ASN P 93 ASN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 GLN P 122 HIS P 130 ASN P 145 HIS P 166 ASN ** P 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 GLN Q 45 GLN ** Q 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 4 HIS ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 85 ASN R 27 ASN ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN S 144 GLN T 54 HIS T 58 HIS V 31 ASN ** V 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 101 ASN X 73 HIS ** X 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 18 HIS Y 65 GLN K 157 GLN ** K 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 HIS K 468 ASN Z 76 ASN a 17 HIS ** a 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 GLN Total number of N/Q/H flips: 98 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1139 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.122 148407 Z= 0.255 Angle : 0.773 16.622 218577 Z= 0.389 Chirality : 0.040 0.321 27200 Planarity : 0.007 0.146 13640 Dihedral : 16.157 179.977 53193 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.77 % Favored : 95.17 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % 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: -0.50 (0.10), residues: 6953 helix: 0.50 (0.10), residues: 2384 sheet: -0.39 (0.17), residues: 935 loop : -0.84 (0.10), residues: 3634 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 470 time to evaluate : 6.554 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: 146 outliers final: 58 residues processed: 579 average time/residue: 1.3412 time to fit residues: 1331.7471 Evaluate side-chains 429 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 371 time to evaluate : 6.321 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 1.0581 time to fit residues: 125.1198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 535 optimal weight: 0.0670 chunk 299 optimal weight: 1.9990 chunk 802 optimal weight: 10.0000 chunk 656 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 966 optimal weight: 9.9990 chunk 1043 optimal weight: 7.9990 chunk 860 optimal weight: 10.0000 chunk 958 optimal weight: 9.9990 chunk 329 optimal weight: 2.9990 chunk 775 optimal weight: 9.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 10 HIS ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS C 38 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 85 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 HIS d 93 ASN ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS F 165 ASN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS ** h 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 107 GLN ** H 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 GLN N 109 HIS N 158 HIS ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS O 199 HIS ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN P 63 GLN p 34 HIS p 72 ASN ** Q 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 12 ASN ** R 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 118 HIS ** S 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 GLN T 98 HIS ** V 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN K 209 HIS a 44 ASN ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1919 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.252 148407 Z= 0.353 Angle : 0.908 20.630 218577 Z= 0.456 Chirality : 0.046 0.655 27200 Planarity : 0.009 0.212 13640 Dihedral : 17.368 179.813 53193 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 28.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.02 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.06 % 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: -1.34 (0.09), residues: 6953 helix: -0.25 (0.10), residues: 2386 sheet: -0.63 (0.19), residues: 754 loop : -1.35 (0.09), residues: 3813 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 469 time to evaluate : 6.570 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 outliers start: 178 outliers final: 77 residues processed: 601 average time/residue: 1.3353 time to fit residues: 1395.6657 Evaluate side-chains 448 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 371 time to evaluate : 6.377 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 1.0353 time to fit residues: 159.9761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 954 optimal weight: 9.9990 chunk 726 optimal weight: 10.0000 chunk 501 optimal weight: 7.9990 chunk 106 optimal weight: 0.2980 chunk 461 optimal weight: 8.9990 chunk 648 optimal weight: 10.0000 chunk 969 optimal weight: 7.9990 chunk 1026 optimal weight: 10.0000 chunk 506 optimal weight: 5.9990 chunk 918 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 15 GLN A 194 ASN ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN C 61 GLN ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN D 244 HIS ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN e 68 HIS e 80 HIS ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 HIS F 41 GLN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN G 66 GLN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 ASN h 30 GLN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN ** I 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 HIS J 65 ASN J 112 HIS ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 17 GLN ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 117 HIS ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 GLN N 117 ASN ** N 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 HIS ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 57 ASN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 23 GLN r 121 GLN ** R 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS ** S 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 ASN T 90 ASN ** V 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 107 HIS ** Y 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 HIS ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 447 HIS a 17 HIS a 34 ASN a 62 HIS a 120 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3083 moved from start: 1.0090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.414 148407 Z= 0.486 Angle : 1.241 32.169 218577 Z= 0.622 Chirality : 0.059 0.876 27200 Planarity : 0.011 0.198 13640 Dihedral : 19.468 179.924 53193 Min Nonbonded Distance : 1.395 Molprobity Statistics. All-atom Clashscore : 38.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.33 % Favored : 90.44 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.22 % 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: -2.77 (0.09), residues: 6953 helix: -1.40 (0.09), residues: 2369 sheet: -1.37 (0.19), residues: 709 loop : -2.26 (0.09), residues: 3875 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 610 time to evaluate : 6.636 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: 299 outliers final: 107 residues processed: 850 average time/residue: 1.2953 time to fit residues: 1886.7313 Evaluate side-chains 572 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 465 time to evaluate : 5.826 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 1.0386 time to fit residues: 213.9484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 854 optimal weight: 9.9990 chunk 582 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 764 optimal weight: 8.9990 chunk 423 optimal weight: 2.9990 chunk 875 optimal weight: 10.0000 chunk 709 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 524 optimal weight: 0.9990 chunk 921 optimal weight: 30.0000 chunk 259 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 69 GLN A 187 HIS A 205 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 119 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 121 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN g 18 ASN G 29 ASN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 GLN ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 HIS ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN I 166 HIS ** j 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 GLN ** M 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN N 139 HIS N 201 HIS ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 36 GLN ** o 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 160 HIS ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 85 ASN r 121 GLN R 40 GLN T 58 HIS ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS U 50 ASN ** V 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 439 ASN ** a 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3451 moved from start: 1.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.268 148407 Z= 0.337 Angle : 0.965 19.706 218577 Z= 0.484 Chirality : 0.048 0.723 27200 Planarity : 0.009 0.148 13640 Dihedral : 18.986 179.776 53193 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 29.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.74 % Favored : 92.20 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % 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: -2.50 (0.09), residues: 6953 helix: -0.89 (0.10), residues: 2420 sheet: -1.58 (0.18), residues: 746 loop : -2.24 (0.09), residues: 3787 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 606 time to evaluate : 6.508 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 outliers start: 189 outliers final: 72 residues processed: 752 average time/residue: 1.3070 time to fit residues: 1694.4014 Evaluate side-chains 574 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 502 time to evaluate : 6.443 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 72 outliers final: 1 residues processed: 72 average time/residue: 1.1128 time to fit residues: 155.3439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 345 optimal weight: 3.9990 chunk 924 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 602 optimal weight: 9.9990 chunk 253 optimal weight: 0.2980 chunk 1027 optimal weight: 10.0000 chunk 852 optimal weight: 20.0000 chunk 475 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 chunk 339 optimal weight: 0.8980 chunk 539 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 GLN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN E 132 HIS ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 ASN F 121 ASN g 18 ASN ** G 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 HIS J 23 ASN J 98 ASN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 201 HIS ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 ASN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 33 GLN ** Q 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 146 HIS ** V 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3359 moved from start: 1.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 148407 Z= 0.180 Angle : 0.700 16.202 218577 Z= 0.355 Chirality : 0.039 0.250 27200 Planarity : 0.006 0.079 13640 Dihedral : 18.353 179.882 53193 Min Nonbonded Distance : 1.025 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.90 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.76 (0.09), residues: 6953 helix: -0.08 (0.10), residues: 2397 sheet: -1.22 (0.18), residues: 758 loop : -1.93 (0.09), residues: 3798 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 600 time to evaluate : 5.839 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: 101 outliers final: 39 residues processed: 670 average time/residue: 1.3318 time to fit residues: 1534.7076 Evaluate side-chains 549 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 510 time to evaluate : 6.527 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 1.1417 time to fit residues: 89.9450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 990 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 585 optimal weight: 10.0000 chunk 750 optimal weight: 20.0000 chunk 581 optimal weight: 9.9990 chunk 864 optimal weight: 10.0000 chunk 573 optimal weight: 5.9990 chunk 1023 optimal weight: 20.0000 chunk 640 optimal weight: 9.9990 chunk 624 optimal weight: 10.0000 chunk 472 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 12 GLN ** b 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 60 ASN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN ** d 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 ASN D 63 GLN D 138 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS ** G 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 HIS ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 HIS ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN l 17 GLN N 8 GLN ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 23 GLN r 83 ASN r 103 HIS ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 HIS ** S 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 58 HIS T 70 HIS ** V 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 57 GLN ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 248 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 GLN ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 28 HIS ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4957 moved from start: 1.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.310 148407 Z= 0.651 Angle : 1.600 27.477 218577 Z= 0.784 Chirality : 0.072 0.658 27200 Planarity : 0.013 0.289 13640 Dihedral : 20.892 179.596 53193 Min Nonbonded Distance : 0.809 Molprobity Statistics. All-atom Clashscore : 46.19 Ramachandran Plot: Outliers : 0.60 % Allowed : 13.12 % Favored : 86.28 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.43 % 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: -3.68 (0.09), residues: 6953 helix: -1.86 (0.09), residues: 2341 sheet: -1.97 (0.18), residues: 716 loop : -3.02 (0.09), residues: 3896 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 954 time to evaluate : 6.545 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 outliers start: 218 outliers final: 79 residues processed: 1121 average time/residue: 1.3268 time to fit residues: 2525.7363 Evaluate side-chains 823 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 744 time to evaluate : 6.471 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 2 residues processed: 79 average time/residue: 1.0895 time to fit residues: 164.9635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 633 optimal weight: 10.0000 chunk 408 optimal weight: 1.9990 chunk 611 optimal weight: 50.0000 chunk 308 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 650 optimal weight: 5.9990 chunk 697 optimal weight: 0.8980 chunk 506 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 804 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 10 HIS ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN B 245 HIS B 289 GLN ** c 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 ASN d 93 ASN D 57 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 101 HIS E 132 HIS ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN F 112 GLN F 153 ASN F 207 ASN ** F 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS I 130 HIS L 15 HIS ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 ASN ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 GLN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 83 ASN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 156 HIS T 3 ASN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 93 ASN Y 20 ASN ** Y 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4829 moved from start: 1.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 148407 Z= 0.283 Angle : 0.905 24.736 218577 Z= 0.457 Chirality : 0.047 0.369 27200 Planarity : 0.007 0.145 13640 Dihedral : 19.546 179.920 53193 Min Nonbonded Distance : 0.922 Molprobity Statistics. All-atom Clashscore : 28.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.66 % Favored : 91.27 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.12 % 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: -2.93 (0.09), residues: 6953 helix: -1.01 (0.10), residues: 2387 sheet: -1.74 (0.18), residues: 746 loop : -2.70 (0.09), residues: 3820 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 844 time to evaluate : 6.622 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: 96 outliers final: 55 residues processed: 901 average time/residue: 1.3659 time to fit residues: 2100.4157 Evaluate side-chains 766 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 711 time to evaluate : 6.530 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 55 outliers final: 1 residues processed: 55 average time/residue: 1.0695 time to fit residues: 117.5501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 931 optimal weight: 20.0000 chunk 980 optimal weight: 10.0000 chunk 894 optimal weight: 9.9990 chunk 953 optimal weight: 10.0000 chunk 574 optimal weight: 9.9990 chunk 415 optimal weight: 5.9990 chunk 749 optimal weight: 20.0000 chunk 292 optimal weight: 7.9990 chunk 861 optimal weight: 9.9990 chunk 902 optimal weight: 10.0000 chunk 950 optimal weight: 3.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 12 GLN b 27 GLN ** b 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 GLN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 101 HIS ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 ASN ** f 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 207 ASN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 ASN i 80 HIS I 92 HIS ** I 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 66 HIS ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 19 GLN N 91 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 57 ASN ** Q 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 ASN T 58 HIS T 70 HIS ** V 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 57 GLN ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 HIS ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS a 41 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 1.9719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.187 148407 Z= 0.553 Angle : 1.351 27.590 218577 Z= 0.670 Chirality : 0.063 0.691 27200 Planarity : 0.011 0.181 13640 Dihedral : 20.326 179.444 53193 Min Nonbonded Distance : 0.894 Molprobity Statistics. All-atom Clashscore : 40.24 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.38 % Favored : 86.21 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.45 % 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: -3.64 (0.09), residues: 6953 helix: -1.68 (0.09), residues: 2350 sheet: -2.11 (0.18), residues: 712 loop : -3.06 (0.09), residues: 3891 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1111 time to evaluate : 6.618 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 outliers start: 117 outliers final: 44 residues processed: 1186 average time/residue: 1.3804 time to fit residues: 2772.9865 Evaluate side-chains 933 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 889 time to evaluate : 8.747 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 1.0519 time to fit residues: 95.1754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 626 optimal weight: 7.9990 chunk 1008 optimal weight: 7.9990 chunk 615 optimal weight: 5.9990 chunk 478 optimal weight: 0.9990 chunk 701 optimal weight: 10.9990 chunk 1058 optimal weight: 2.9990 chunk 973 optimal weight: 0.7980 chunk 842 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 650 optimal weight: 5.9990 chunk 516 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN B 322 HIS B 328 ASN ** c 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 HIS ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 237 ASN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS G 153 GLN G 195 HIS i 12 ASN I 92 HIS ** j 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN M 125 ASN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 36 GLN o 45 GLN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 HIS ** p 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 57 ASN ** Q 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 4 HIS r 6 GLN ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 ASN S 125 GLN U 116 GLN ** V 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 100 HIS ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 GLN ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5344 moved from start: 1.9517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 148407 Z= 0.219 Angle : 0.843 20.979 218577 Z= 0.425 Chirality : 0.044 0.443 27200 Planarity : 0.007 0.091 13640 Dihedral : 19.304 179.738 53193 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.08 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.74 (0.09), residues: 6953 helix: -0.79 (0.10), residues: 2388 sheet: -1.69 (0.18), residues: 700 loop : -2.62 (0.09), residues: 3865 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13906 Ramachandran restraints generated. 6953 Oldfield, 0 Emsley, 6953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1028 time to evaluate : 6.600 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 outliers start: 44 outliers final: 17 residues processed: 1049 average time/residue: 1.3323 time to fit residues: 2428.1069 Evaluate side-chains 887 residues out of total 6064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 870 time to evaluate : 6.634 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 1.1285 time to fit residues: 43.3758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 669 optimal weight: 20.0000 chunk 897 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 776 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 843 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 866 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 155 optimal weight: 0.0030 overall best weight: 5.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 GLN B 55 HIS ** B 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS F 112 GLN F 153 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN G 64 GLN G 66 GLN ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN G 85 GLN G 100 HIS h 96 ASN H 162 GLN i 12 ASN ** j 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 HIS ** L 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN M 34 ASN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 GLN ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 105 GLN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 ASN ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 ASN Q 57 ASN ** r 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 HIS T 3 ASN ** V 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.197260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.177536 restraints weight = 281969.287| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 1.58 r_work: 0.4053 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 2.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.169 148407 Z= 0.416 Angle : 1.074 22.169 218577 Z= 0.536 Chirality : 0.053 0.450 27200 Planarity : 0.009 0.144 13640 Dihedral : 19.483 179.697 53193 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.43 % Favored : 88.38 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.98 (0.09), residues: 6953 helix: -1.02 (0.10), residues: 2392 sheet: -1.81 (0.18), residues: 735 loop : -2.75 (0.09), residues: 3826 =============================================================================== Job complete usr+sys time: 30094.46 seconds wall clock time: 531 minutes 45.09 seconds (31905.09 seconds total)