Starting phenix.real_space_refine on Wed Mar 20 06:12:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo3_13004/03_2024/7oo3_13004_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo3_13004/03_2024/7oo3_13004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo3_13004/03_2024/7oo3_13004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo3_13004/03_2024/7oo3_13004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo3_13004/03_2024/7oo3_13004_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo3_13004/03_2024/7oo3_13004_trim.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2273 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 92 5.49 5 Mg 1 5.21 5 S 281 5.16 5 C 30866 2.51 5 N 8653 2.21 5 O 9489 1.98 5 H 46456 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 483": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1073": "OE1" <-> "OE2" Residue "A ARG 1149": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A ARG 1258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1333": "OE1" <-> "OE2" Residue "A ARG 1375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1433": "OE1" <-> "OE2" Residue "A GLU 1434": "OE1" <-> "OE2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B ARG 638": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B GLU 826": "OE1" <-> "OE2" Residue "B GLU 827": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "H ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "K GLU 8": "OE1" <-> "OE2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "a GLU 74": "OE1" <-> "OE2" Residue "a GLU 141": "OE1" <-> "OE2" Residue "a GLU 188": "OE1" <-> "OE2" Residue "a GLU 238": "OE1" <-> "OE2" Residue "a GLU 278": "OE1" <-> "OE2" Residue "a GLU 306": "OE1" <-> "OE2" Residue "b GLU 492": "OE1" <-> "OE2" Residue "b ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 562": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 564": "OE1" <-> "OE2" Residue "b GLU 584": "OE1" <-> "OE2" Residue "b ARG 593": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 637": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 652": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 666": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 767": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 876": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 903": "OE1" <-> "OE2" Residue "b ARG 915": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 946": "OE1" <-> "OE2" Residue "b ARG 950": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 969": "OE1" <-> "OE2" Residue "b ARG 985": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 993": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 1003": "OE1" <-> "OE2" Residue "d GLU 27": "OE1" <-> "OE2" Residue "d GLU 40": "OE1" <-> "OE2" Residue "d GLU 54": "OE1" <-> "OE2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d GLU 151": "OE1" <-> "OE2" Residue "d GLU 199": "OE1" <-> "OE2" Residue "d GLU 210": "OE1" <-> "OE2" Residue "d GLU 277": "OE1" <-> "OE2" Residue "d GLU 288": "OE1" <-> "OE2" Residue "d GLU 303": "OE1" <-> "OE2" Residue "d GLU 368": "OE1" <-> "OE2" Residue "d GLU 706": "OE1" <-> "OE2" Residue "d GLU 719": "OE1" <-> "OE2" Residue "d GLU 728": "OE1" <-> "OE2" Residue "d GLU 800": "OE1" <-> "OE2" Residue "d GLU 839": "OE1" <-> "OE2" Residue "d GLU 840": "OE1" <-> "OE2" Residue "d GLU 865": "OE1" <-> "OE2" Residue "d GLU 898": "OE1" <-> "OE2" Residue "d GLU 987": "OE1" <-> "OE2" Residue "d GLU 1045": "OE1" <-> "OE2" Residue "d GLU 1069": "OE1" <-> "OE2" Residue "d GLU 1079": "OE1" <-> "OE2" Residue "d GLU 1095": "OE1" <-> "OE2" Residue "d GLU 1134": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 95846 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 22493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 22493 Classifications: {'peptide': 1412} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1342} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 18140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 18140 Classifications: {'peptide': 1131} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Chain: "C" Number of atoms: 4119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 4119 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 15, 'TRANS': 244} Chain breaks: 1 Chain: "D" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2046 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "E" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3457 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 197} Chain: "F" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1341 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2709 Classifications: {'peptide': 171} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2333 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1828 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1086 Classifications: {'peptide': 67} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1862 Classifications: {'peptide': 115} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 781 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 727 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "T" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 947 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "P" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 329 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "a" Number of atoms: 5541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5541 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 355} Chain: "b" Number of atoms: 8744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8744 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 21, 'TRANS': 512} Chain breaks: 3 Chain: "x" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 175 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UNK:plan-1': 35} Unresolved non-hydrogen planarities: 35 Chain: "c" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 707 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 8} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 133} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 615 Unresolved non-hydrogen angles: 874 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 290 Chain: "d" Number of atoms: 16472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 16472 Classifications: {'peptide': 1096} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1055} Chain breaks: 6 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 942 SG CYS A 71 43.087 107.725 101.384 1.00 52.69 S ATOM 983 SG CYS A 74 43.443 111.313 101.544 1.00 47.16 S ATOM 1070 SG CYS A 81 44.500 110.110 98.639 1.00 42.39 S ATOM 1553 SG CYS A 111 86.743 98.401 117.284 1.00 80.61 S ATOM 2262 SG CYS A 154 88.920 100.118 119.235 1.00 89.30 S ATOM 2300 SG CYS A 184 88.394 96.436 120.357 1.00 93.10 S ATOM 39752 SG CYS B1119 54.988 118.223 111.173 1.00 41.49 S ATOM 39795 SG CYS B1122 57.219 115.578 109.818 1.00 39.35 S ATOM 40020 SG CYS B1137 53.965 114.558 110.215 1.00 52.03 S ATOM 40061 SG CYS B1140 56.785 115.871 113.108 1.00 51.52 S ATOM 42014 SG CYS C 88 15.641 130.300 42.641 1.00 42.36 S ATOM 42038 SG CYS C 90 15.152 127.458 44.509 1.00 48.37 S ATOM 42098 SG CYS C 94 14.562 127.782 41.430 1.00 34.57 S ATOM 42137 SG CYS C 97 18.354 127.603 41.962 1.00 31.58 S ATOM 56771 SG CYS I 17 119.714 68.714 69.229 1.00 77.75 S ATOM 56813 SG CYS I 20 116.603 69.044 71.008 1.00 77.23 S ATOM 57134 SG CYS I 39 117.988 71.248 72.651 1.00 79.41 S ATOM 57182 SG CYS I 42 119.813 68.155 72.184 1.00 81.69 S ATOM 57855 SG CYS I 86 114.504 92.043 31.637 1.00 52.66 S ATOM 57904 SG CYS I 89 113.406 89.950 29.214 1.00 55.55 S ATOM 58296 SG CYS I 114 110.847 90.839 30.852 1.00 45.61 S ATOM 58361 SG CYS I 119 113.486 88.250 32.006 1.00 53.66 S ATOM 58583 SG CYS J 7 46.648 121.889 30.452 1.00 11.22 S ATOM 58627 SG CYS J 10 45.012 124.604 28.682 1.00 9.29 S ATOM 59152 SG CYS J 44 48.849 124.031 28.570 1.00 11.31 S ATOM 59162 SG CYS J 45 46.446 122.234 26.591 1.00 11.02 S ATOM 61526 SG CYS L 19 31.577 84.935 48.796 1.00 54.66 S ATOM 61558 SG CYS L 22 29.264 83.724 46.847 1.00 59.22 S ATOM 61788 SG CYS L 36 28.389 83.082 49.882 1.00 61.25 S ATOM 61837 SG CYS L 39 31.729 81.387 48.141 1.00 65.09 S Time building chain proxies: 33.52, per 1000 atoms: 0.35 Number of scatterers: 95846 At special positions: 0 Unit cell: (155.4, 198.45, 239.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 281 16.00 P 92 15.00 Mg 1 11.99 O 9489 8.00 N 8653 7.00 C 30866 6.00 H 46456 1.00 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: 60.31 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 39 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11096 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 85 sheets defined 34.0% alpha, 23.2% beta 40 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 36.68 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.840A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.742A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.987A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.717A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.567A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.915A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.752A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.990A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.662A pdb=" N SER A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 4.171A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.840A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.844A pdb=" N ARG A1149 " --> pdb=" O GLY A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.718A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.588A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1280 through 1296 removed outlier: 4.000A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 4.095A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.827A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.588A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.719A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.255A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.550A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.570A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.834A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.678A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.818A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 removed outlier: 3.560A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.796A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.530A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1164 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.587A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.106A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.505A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.883A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 90 removed outlier: 3.970A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.528A pdb=" N LEU D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.727A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.614A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 4.215A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.552A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.040A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'a' and resid 2 through 10 Processing helix chain 'a' and resid 14 through 29 removed outlier: 3.800A pdb=" N LEU a 18 " --> pdb=" O ASP a 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 500 through 505 Processing helix chain 'b' and resid 508 through 525 Processing helix chain 'b' and resid 538 through 552 Processing helix chain 'b' and resid 574 through 576 No H-bonds generated for 'chain 'b' and resid 574 through 576' Processing helix chain 'b' and resid 577 through 589 Processing helix chain 'b' and resid 606 through 617 Processing helix chain 'b' and resid 624 through 631 Processing helix chain 'b' and resid 648 through 652 Processing helix chain 'b' and resid 656 through 663 Processing helix chain 'b' and resid 681 through 693 removed outlier: 4.162A pdb=" N LEU b 685 " --> pdb=" O ASN b 681 " (cutoff:3.500A) Processing helix chain 'b' and resid 699 through 714 removed outlier: 5.429A pdb=" N VAL b 709 " --> pdb=" O GLU b 705 " (cutoff:3.500A) Proline residue: b 710 - end of helix Processing helix chain 'b' and resid 720 through 739 Processing helix chain 'b' and resid 769 through 782 Processing helix chain 'b' and resid 782 through 790 removed outlier: 3.697A pdb=" N TYR b 786 " --> pdb=" O SER b 782 " (cutoff:3.500A) Processing helix chain 'b' and resid 794 through 808 removed outlier: 4.209A pdb=" N GLY b 798 " --> pdb=" O GLN b 794 " (cutoff:3.500A) Processing helix chain 'b' and resid 808 through 814 removed outlier: 3.959A pdb=" N PHE b 812 " --> pdb=" O HIS b 808 " (cutoff:3.500A) Processing helix chain 'b' and resid 834 through 837 Processing helix chain 'b' and resid 838 through 855 Processing helix chain 'b' and resid 864 through 878 Processing helix chain 'b' and resid 890 through 892 No H-bonds generated for 'chain 'b' and resid 890 through 892' Processing helix chain 'b' and resid 893 through 904 removed outlier: 3.981A pdb=" N LEU b 897 " --> pdb=" O SER b 893 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP b 904 " --> pdb=" O ARG b 900 " (cutoff:3.500A) Processing helix chain 'b' and resid 937 through 949 removed outlier: 3.917A pdb=" N ASP b 941 " --> pdb=" O ASN b 937 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA b 948 " --> pdb=" O ALA b 944 " (cutoff:3.500A) Processing helix chain 'b' and resid 967 through 988 removed outlier: 3.532A pdb=" N LYS b 971 " --> pdb=" O THR b 967 " (cutoff:3.500A) Processing helix chain 'b' and resid 997 through 1003 Processing helix chain 'b' and resid 1016 through 1022 Processing helix chain 'b' and resid 1387 through 1399 removed outlier: 3.676A pdb=" N LEU b1399 " --> pdb=" O ALA b1395 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 12 Processing helix chain 'x' and resid 22 through 30 removed outlier: 3.795A pdb=" N UNK x 28 " --> pdb=" O UNK x 24 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N UNK x 30 " --> pdb=" O UNK x 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 14 removed outlier: 3.513A pdb=" N THR c 14 " --> pdb=" O GLU c 10 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 35 Processing helix chain 'c' and resid 36 through 51 removed outlier: 3.532A pdb=" N SER c 40 " --> pdb=" O GLU c 36 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG c 41 " --> pdb=" O GLU c 37 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG c 44 " --> pdb=" O SER c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 71 Processing helix chain 'c' and resid 75 through 80 Processing helix chain 'c' and resid 83 through 94 removed outlier: 3.702A pdb=" N ASP c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 124 removed outlier: 4.130A pdb=" N GLU c 122 " --> pdb=" O GLU c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 141 Processing helix chain 'd' and resid 250 through 254 Processing helix chain 'd' and resid 366 through 370 removed outlier: 4.219A pdb=" N GLN d 370 " --> pdb=" O LEU d 367 " (cutoff:3.500A) Processing helix chain 'd' and resid 756 through 760 removed outlier: 3.922A pdb=" N ALA d 760 " --> pdb=" O SER d 757 " (cutoff:3.500A) Processing helix chain 'd' and resid 986 through 991 Processing helix chain 'd' and resid 1044 through 1062 Processing helix chain 'd' and resid 1069 through 1074 Processing helix chain 'd' and resid 1091 through 1096 Processing helix chain 'd' and resid 1097 through 1100 removed outlier: 4.047A pdb=" N ILE d1100 " --> pdb=" O PHE d1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 1097 through 1100' Processing helix chain 'd' and resid 1101 through 1109 Processing helix chain 'd' and resid 1125 through 1138 removed outlier: 3.691A pdb=" N LEU d1129 " --> pdb=" O THR d1125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.522A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.850A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.389A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.717A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1060 through 1061 removed outlier: 6.063A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.992A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.773A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.147A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.147A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 603 removed outlier: 6.710A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB8, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB9, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.812A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.511A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.587A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR A1177 " --> pdb=" O PRO A1209 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC4, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 8.315A pdb=" N GLY A1409 " --> pdb=" O GLN E 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC6, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AC7, first strand: chain 'B' and resid 87 through 93 removed outlier: 5.725A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 132 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AD2, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.659A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD5, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.539A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.693A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.693A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD9, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.367A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AE2, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.904A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AE4, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE5, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.632A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.966A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE8, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.744A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.744A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.093A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AF3, first strand: chain 'G' and resid 83 through 92 removed outlier: 6.717A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AF5, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AF6, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF7, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.623A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 30 through 32 removed outlier: 3.634A pdb=" N CYS a 339 " --> pdb=" O GLY a 352 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 36 through 38 removed outlier: 7.334A pdb=" N ASP a 37 " --> pdb=" O CYS a 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.271A pdb=" N ASP a 72 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA a 86 " --> pdb=" O ASP a 72 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 102 through 107 removed outlier: 3.948A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL a 137 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL a 126 " --> pdb=" O ALA a 135 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 144 through 149 Processing sheet with id=AG4, first strand: chain 'a' and resid 189 through 194 Processing sheet with id=AG5, first strand: chain 'a' and resid 248 through 253 removed outlier: 3.651A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 298 through 299 removed outlier: 6.386A pdb=" N THR a 320 " --> pdb=" O GLN a 326 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLN a 326 " --> pdb=" O THR a 320 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 594 through 596 removed outlier: 6.301A pdb=" N THR b 569 " --> pdb=" O LEU b 621 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N THR b 623 " --> pdb=" O THR b 569 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE b 571 " --> pdb=" O THR b 623 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE b 529 " --> pdb=" O LEU b 743 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 882 through 884 removed outlier: 7.053A pdb=" N LEU b 883 " --> pdb=" O LEU b 911 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL b 929 " --> pdb=" O TYR b 960 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU b 962 " --> pdb=" O VAL b 929 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE b 931 " --> pdb=" O LEU b 962 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN b 760 " --> pdb=" O VAL b 959 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ARG b 961 " --> pdb=" O ASN b 760 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN b 762 " --> pdb=" O ARG b 961 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU b 963 " --> pdb=" O GLN b 762 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU b 764 " --> pdb=" O LEU b 963 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 1004 through 1009 removed outlier: 5.473A pdb=" N GLY d1026 " --> pdb=" O SER d1042 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER d1042 " --> pdb=" O GLY d1026 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE d1037 " --> pdb=" O ALA d 9 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN d 4 " --> pdb=" O ILE d1089 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'd' and resid 15 through 21 removed outlier: 5.917A pdb=" N VAL d 43 " --> pdb=" O PRO d 51 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 61 through 67 removed outlier: 4.009A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA d 86 " --> pdb=" O HIS d 105 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N HIS d 105 " --> pdb=" O ALA d 86 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE d 88 " --> pdb=" O ARG d 103 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 121 through 124 Processing sheet with id=AH4, first strand: chain 'd' and resid 164 through 169 removed outlier: 5.642A pdb=" N VAL d 164 " --> pdb=" O GLN d 183 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN d 183 " --> pdb=" O VAL d 164 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 164 through 169 removed outlier: 5.642A pdb=" N VAL d 164 " --> pdb=" O GLN d 183 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN d 183 " --> pdb=" O VAL d 164 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 218 through 221 Processing sheet with id=AH7, first strand: chain 'd' and resid 258 through 263 removed outlier: 4.505A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU d 280 " --> pdb=" O LEU d 305 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU d 288 " --> pdb=" O LEU d 297 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU d 297 " --> pdb=" O GLU d 288 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 313 through 318 removed outlier: 6.504A pdb=" N VAL d 321 " --> pdb=" O LEU d 317 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LYS d 335 " --> pdb=" O ALA d 349 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA d 349 " --> pdb=" O LYS d 335 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'd' and resid 361 through 364 removed outlier: 4.078A pdb=" N ASP d 361 " --> pdb=" O CYS d 378 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'd' and resid 398 through 400 removed outlier: 3.677A pdb=" N ALA d 400 " --> pdb=" O ILE d 701 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'd' and resid 410 through 413 removed outlier: 3.846A pdb=" N VAL d 435 " --> pdb=" O THR d 446 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'd' and resid 457 through 463 removed outlier: 4.262A pdb=" N SER d 475 " --> pdb=" O THR d 472 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER d 488 " --> pdb=" O LEU d 478 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'd' and resid 507 through 512 removed outlier: 4.000A pdb=" N SER d 530 " --> pdb=" O TYR d 518 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN d 520 " --> pdb=" O GLN d 528 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN d 528 " --> pdb=" O GLN d 520 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N HIS d 522 " --> pdb=" O LEU d 526 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU d 526 " --> pdb=" O HIS d 522 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'd' and resid 538 through 542 removed outlier: 6.265A pdb=" N GLY d 559 " --> pdb=" O ALA d 539 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU d 541 " --> pdb=" O ALA d 557 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA d 557 " --> pdb=" O LEU d 541 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU d 560 " --> pdb=" O SER d 565 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER d 565 " --> pdb=" O LEU d 560 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS d 578 " --> pdb=" O ILE d 568 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS d 570 " --> pdb=" O LEU d 576 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU d 576 " --> pdb=" O LYS d 570 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'd' and resid 588 through 595 removed outlier: 3.962A pdb=" N HIS d 600 " --> pdb=" O LEU d 616 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA d 610 " --> pdb=" O LEU d 606 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU d 611 " --> pdb=" O LYS d 628 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS d 628 " --> pdb=" O LEU d 611 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR d 613 " --> pdb=" O ARG d 626 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG d 626 " --> pdb=" O TYR d 613 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'd' and resid 637 through 642 removed outlier: 3.570A pdb=" N PHE d 641 " --> pdb=" O ASN d 648 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR d 647 " --> pdb=" O SER d 661 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N SER d 661 " --> pdb=" O THR d 647 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.440A pdb=" N LEU d 736 " --> pdb=" O ARG d 722 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE d 724 " --> pdb=" O GLY d 734 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY d 734 " --> pdb=" O ILE d 724 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR d 726 " --> pdb=" O CYS d 732 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N CYS d 732 " --> pdb=" O TYR d 726 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP d 795 " --> pdb=" O VAL d 801 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL d 801 " --> pdb=" O ASP d 795 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER d 764 " --> pdb=" O GLN d 806 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'd' and resid 811 through 819 removed outlier: 6.659A pdb=" N GLY d 832 " --> pdb=" O LEU d 814 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU d 816 " --> pdb=" O ILE d 830 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE d 830 " --> pdb=" O LEU d 816 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER d 818 " --> pdb=" O TYR d 828 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR d 828 " --> pdb=" O SER d 818 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN d 852 " --> pdb=" O THR d 860 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR d 860 " --> pdb=" O GLN d 852 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N SER d 854 " --> pdb=" O LEU d 858 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU d 858 " --> pdb=" O SER d 854 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'd' and resid 872 through 876 removed outlier: 4.034A pdb=" N SER d 872 " --> pdb=" O SER d 883 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL d 888 " --> pdb=" O ASN d 904 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN d 904 " --> pdb=" O VAL d 888 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU d 890 " --> pdb=" O GLU d 902 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'd' and resid 911 through 917 removed outlier: 4.557A pdb=" N VAL d 930 " --> pdb=" O ASP d 948 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA d 934 " --> pdb=" O GLU d 944 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU d 944 " --> pdb=" O ALA d 934 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'd' and resid 954 through 959 removed outlier: 3.631A pdb=" N ALA d 956 " --> pdb=" O ALA d 968 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN d 973 " --> pdb=" O GLU d 969 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN d 978 " --> pdb=" O GLU d 994 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU d 994 " --> pdb=" O GLN d 978 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'd' and resid 1076 through 1078 2061 hydrogen bonds defined for protein. 5685 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 49.01 Time building geometry restraints manager: 63.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 46362 1.02 - 1.22: 135 1.22 - 1.42: 20759 1.42 - 1.61: 29276 1.61 - 1.81: 437 Bond restraints: 96969 Sorted by residual: bond pdb=" CG1 ILE d 659 " pdb=" CD1 ILE d 659 " ideal model delta sigma weight residual 1.513 1.257 0.256 3.90e-02 6.57e+02 4.31e+01 bond pdb=" CD1 ILE d 659 " pdb="HD13 ILE d 659 " ideal model delta sigma weight residual 0.970 0.855 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" CG LEU d 623 " pdb=" CD2 LEU d 623 " ideal model delta sigma weight residual 1.521 1.332 0.189 3.30e-02 9.18e+02 3.29e+01 bond pdb=" CG1 ILE d 407 " pdb=" CD1 ILE d 407 " ideal model delta sigma weight residual 1.513 1.341 0.172 3.90e-02 6.57e+02 1.95e+01 bond pdb=" CD2 LEU d 616 " pdb="HD21 LEU d 616 " ideal model delta sigma weight residual 0.970 0.888 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 96964 not shown) Histogram of bond angle deviations from ideal: 93.55 - 101.72: 206 101.72 - 109.89: 76963 109.89 - 118.05: 52429 118.05 - 126.22: 43502 126.22 - 134.39: 1227 Bond angle restraints: 174327 Sorted by residual: angle pdb=" N ASP d 705 " pdb=" CA ASP d 705 " pdb=" C ASP d 705 " ideal model delta sigma weight residual 111.14 117.68 -6.54 1.08e+00 8.57e-01 3.66e+01 angle pdb=" N ILE d 707 " pdb=" CA ILE d 707 " pdb=" C ILE d 707 " ideal model delta sigma weight residual 109.34 121.19 -11.85 2.08e+00 2.31e-01 3.24e+01 angle pdb=" N VAL d 930 " pdb=" CA VAL d 930 " pdb=" CB VAL d 930 " ideal model delta sigma weight residual 111.23 120.57 -9.34 1.65e+00 3.67e-01 3.21e+01 angle pdb=" CB ILE d 394 " pdb=" CG1 ILE d 394 " pdb=" CD1 ILE d 394 " ideal model delta sigma weight residual 113.80 102.13 11.67 2.10e+00 2.27e-01 3.09e+01 angle pdb=" N SER d 929 " pdb=" CA SER d 929 " pdb=" C SER d 929 " ideal model delta sigma weight residual 110.80 122.47 -11.67 2.13e+00 2.20e-01 3.00e+01 ... (remaining 174322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 44223 35.98 - 71.96: 1273 71.96 - 107.95: 45 107.95 - 143.93: 0 143.93 - 179.91: 7 Dihedral angle restraints: 45548 sinusoidal: 25531 harmonic: 20017 Sorted by residual: dihedral pdb=" CA PHE b 995 " pdb=" C PHE b 995 " pdb=" N PHE b 996 " pdb=" CA PHE b 996 " ideal model delta harmonic sigma weight residual 180.00 136.66 43.34 0 5.00e+00 4.00e-02 7.51e+01 dihedral pdb=" CA LEU b 912 " pdb=" C LEU b 912 " pdb=" N THR b 913 " pdb=" CA THR b 913 " ideal model delta harmonic sigma weight residual 180.00 146.37 33.63 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CA LYS a 174 " pdb=" C LYS a 174 " pdb=" N SER a 175 " pdb=" CA SER a 175 " ideal model delta harmonic sigma weight residual -180.00 -147.28 -32.72 0 5.00e+00 4.00e-02 4.28e+01 ... (remaining 45545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 6747 0.087 - 0.174: 837 0.174 - 0.260: 49 0.260 - 0.347: 9 0.347 - 0.434: 2 Chirality restraints: 7644 Sorted by residual: chirality pdb=" CA GLU d 706 " pdb=" N GLU d 706 " pdb=" C GLU d 706 " pdb=" CB GLU d 706 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CG LEU d 616 " pdb=" CB LEU d 616 " pdb=" CD1 LEU d 616 " pdb=" CD2 LEU d 616 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA PHE d 596 " pdb=" N PHE d 596 " pdb=" C PHE d 596 " pdb=" CB PHE d 596 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 7641 not shown) Planarity restraints: 14321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE d 668 " 0.040 2.00e-02 2.50e+03 3.41e-02 3.50e+01 pdb=" CG PHE d 668 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE d 668 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE d 668 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE d 668 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 PHE d 668 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE d 668 " 0.056 2.00e-02 2.50e+03 pdb=" HD1 PHE d 668 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE d 668 " -0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE d 668 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE d 668 " 0.013 2.00e-02 2.50e+03 pdb=" HZ PHE d 668 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 660 " -0.039 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR d 660 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR d 660 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR d 660 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR d 660 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR d 660 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR d 660 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR d 660 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 TYR d 660 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 TYR d 660 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR d 660 " -0.027 2.00e-02 2.50e+03 pdb=" HE2 TYR d 660 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE d 587 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO d 588 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO d 588 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO d 588 " -0.058 5.00e-02 4.00e+02 ... (remaining 14318 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 3567 2.16 - 2.77: 187228 2.77 - 3.38: 273587 3.38 - 3.99: 373128 3.99 - 4.60: 575041 Nonbonded interactions: 1412551 Sorted by model distance: nonbonded pdb="HH12 ARG a 17 " pdb=" O GLU d 117 " model vdw 1.550 1.850 nonbonded pdb=" OE1 GLU d 719 " pdb=" HG SER d 737 " model vdw 1.571 1.850 nonbonded pdb=" OE2 GLU d 875 " pdb=" H GLY d 878 " model vdw 1.575 1.850 nonbonded pdb=" OG1 THR b 964 " pdb=" HG1 THR b 967 " model vdw 1.608 1.850 nonbonded pdb=" OD1 ASP a 121 " pdb=" HG1 THR a 123 " model vdw 1.610 1.850 ... (remaining 1412546 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.440 Construct map_model_manager: 1.030 Extract box with map and model: 15.660 Check model and map are aligned: 1.080 Set scattering table: 0.640 Process input model: 302.210 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 337.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.010 0.256 50513 Z= 0.636 Angle : 0.896 12.401 68634 Z= 0.479 Chirality : 0.055 0.434 7644 Planarity : 0.005 0.107 8595 Dihedral : 15.286 178.458 19197 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.32 (0.10), residues: 5954 helix: -0.09 (0.12), residues: 1826 sheet: -1.16 (0.14), residues: 1272 loop : -1.17 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP b 589 HIS 0.023 0.002 HIS d 105 PHE 0.059 0.003 PHE d 668 TYR 0.057 0.002 TYR d 660 ARG 0.016 0.001 ARG I 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 839 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 839 time to evaluate : 5.922 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: E 98 ASN cc_start: 0.7516 (t0) cc_final: 0.7304 (t0) REVERT: E 108 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6954 (tm-30) REVERT: L 34 ILE cc_start: 0.8230 (mm) cc_final: 0.8015 (mp) REVERT: b 868 LEU cc_start: 0.8099 (tt) cc_final: 0.7886 (tp) REVERT: d 112 ILE cc_start: 0.8336 (tt) cc_final: 0.8113 (pt) REVERT: d 469 ILE cc_start: 0.7960 (tp) cc_final: 0.7718 (pp) REVERT: d 581 MET cc_start: 0.7178 (tpp) cc_final: 0.6959 (mmp) REVERT: d 650 PHE cc_start: 0.8073 (t80) cc_final: 0.7806 (t80) outliers start: 0 outliers final: 2 residues processed: 839 average time/residue: 3.0083 time to fit residues: 3154.0647 Evaluate side-chains 641 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 639 time to evaluate : 5.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 977 ILE Chi-restraints excluded: chain d residue 286 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 511 optimal weight: 0.5980 chunk 459 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 474 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 288 optimal weight: 40.0000 chunk 353 optimal weight: 5.9990 chunk 550 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 531 ASN A1077 ASN A1101 GLN B 593 GLN B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 GLN C 111 GLN E 95 GLN G 9 HIS I 18 GLN K 55 GLN a 187 GLN a 345 ASN b 616 HIS b 807 ASN b 976 GLN d 372 GLN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 970 ASN ** d1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 50513 Z= 0.215 Angle : 0.570 10.359 68634 Z= 0.301 Chirality : 0.043 0.185 7644 Planarity : 0.004 0.069 8595 Dihedral : 12.721 175.263 7615 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.14 % Allowed : 8.57 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.81 (0.11), residues: 5954 helix: 0.63 (0.12), residues: 1820 sheet: -1.00 (0.14), residues: 1245 loop : -1.02 (0.11), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP d 207 HIS 0.011 0.001 HIS b 616 PHE 0.019 0.001 PHE d 851 TYR 0.017 0.001 TYR b 932 ARG 0.007 0.000 ARG A 928 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 718 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 659 time to evaluate : 6.273 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: A 343 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7936 (pp) REVERT: A 1149 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7450 (mpp-170) REVERT: B 611 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: C 265 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.7068 (m90) REVERT: H 74 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: b 868 LEU cc_start: 0.8082 (tt) cc_final: 0.7845 (tp) REVERT: d 255 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7545 (mp-120) REVERT: d 581 MET cc_start: 0.7263 (tpp) cc_final: 0.7014 (mmp) REVERT: d 845 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7413 (mt0) REVERT: d 1138 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7398 (tpp80) outliers start: 59 outliers final: 28 residues processed: 685 average time/residue: 2.9541 time to fit residues: 2545.9485 Evaluate side-chains 646 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 612 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 187 ARG Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 241 ASN Chi-restraints excluded: chain b residue 577 VAL Chi-restraints excluded: chain b residue 617 CYS Chi-restraints excluded: chain b residue 618 HIS Chi-restraints excluded: chain b residue 623 THR Chi-restraints excluded: chain b residue 913 THR Chi-restraints excluded: chain d residue 236 SER Chi-restraints excluded: chain d residue 254 LYS Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 286 GLU Chi-restraints excluded: chain d residue 659 ILE Chi-restraints excluded: chain d residue 845 GLN Chi-restraints excluded: chain d residue 1105 MET Chi-restraints excluded: chain d residue 1111 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 305 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 458 optimal weight: 5.9990 chunk 374 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 551 optimal weight: 4.9990 chunk 595 optimal weight: 2.9990 chunk 490 optimal weight: 50.0000 chunk 546 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 442 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN B 593 GLN B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN I 18 GLN I 45 GLN a 345 ASN b 616 HIS d 319 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 50513 Z= 0.399 Angle : 0.593 11.135 68634 Z= 0.314 Chirality : 0.044 0.191 7644 Planarity : 0.005 0.068 8595 Dihedral : 12.658 177.884 7613 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.43 % Allowed : 10.44 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -0.64 (0.11), residues: 5954 helix: 0.79 (0.12), residues: 1823 sheet: -0.86 (0.14), residues: 1236 loop : -0.95 (0.11), residues: 2895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP d 207 HIS 0.010 0.001 HIS a 180 PHE 0.024 0.002 PHE d1097 TYR 0.019 0.002 TYR J 43 ARG 0.008 0.001 ARG a 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 708 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 634 time to evaluate : 5.939 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: A 343 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.7921 (pp) REVERT: A 1149 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7543 (mpp-170) REVERT: B 611 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: E 98 ASN cc_start: 0.7400 (t0) cc_final: 0.7194 (t0) REVERT: I 14 ILE cc_start: 0.8696 (tt) cc_final: 0.8316 (tt) REVERT: a 16 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7786 (tt) REVERT: b 853 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5218 (tttt) REVERT: b 923 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7591 (mp) REVERT: d 255 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7411 (mp-120) REVERT: d 845 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: d 993 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7182 (mp10) outliers start: 74 outliers final: 31 residues processed: 674 average time/residue: 2.9867 time to fit residues: 2530.0168 Evaluate side-chains 649 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 610 time to evaluate : 5.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain b residue 520 GLU Chi-restraints excluded: chain b residue 577 VAL Chi-restraints excluded: chain b residue 587 THR Chi-restraints excluded: chain b residue 617 CYS Chi-restraints excluded: chain b residue 618 HIS Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 853 LYS Chi-restraints excluded: chain b residue 913 THR Chi-restraints excluded: chain b residue 923 LEU Chi-restraints excluded: chain b residue 964 THR Chi-restraints excluded: chain d residue 236 SER Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 460 CYS Chi-restraints excluded: chain d residue 659 ILE Chi-restraints excluded: chain d residue 675 GLU Chi-restraints excluded: chain d residue 845 GLN Chi-restraints excluded: chain d residue 993 GLN Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1105 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 544 optimal weight: 9.9990 chunk 414 optimal weight: 10.0000 chunk 286 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 370 optimal weight: 0.6980 chunk 553 optimal weight: 10.0000 chunk 585 optimal weight: 2.9990 chunk 289 optimal weight: 20.0000 chunk 524 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 341 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 593 GLN B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN C 111 GLN I 18 GLN a 345 ASN b 616 HIS b 974 HIS d 163 HIS d 319 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 50513 Z= 0.308 Angle : 0.552 10.527 68634 Z= 0.292 Chirality : 0.043 0.175 7644 Planarity : 0.004 0.068 8595 Dihedral : 12.419 175.684 7610 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.14 % Allowed : 11.81 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 5954 helix: 0.98 (0.12), residues: 1814 sheet: -0.80 (0.14), residues: 1231 loop : -0.86 (0.11), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 207 HIS 0.009 0.001 HIS a 180 PHE 0.017 0.002 PHE d1030 TYR 0.017 0.001 TYR J 43 ARG 0.008 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 694 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 635 time to evaluate : 5.932 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: A 343 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.7916 (pp) REVERT: B 394 ASP cc_start: 0.7792 (t0) cc_final: 0.7490 (t0) REVERT: B 611 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: E 98 ASN cc_start: 0.7479 (t0) cc_final: 0.7240 (t0) REVERT: L 42 ARG cc_start: 0.7646 (mmt90) cc_final: 0.7389 (mmt90) REVERT: a 16 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7801 (tt) REVERT: b 923 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7586 (mp) REVERT: d 581 MET cc_start: 0.7205 (tpp) cc_final: 0.6923 (mmp) REVERT: d 655 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7904 (mmm160) REVERT: d 845 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: d 993 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7163 (mp10) outliers start: 59 outliers final: 30 residues processed: 675 average time/residue: 2.9608 time to fit residues: 2519.5308 Evaluate side-chains 646 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 610 time to evaluate : 5.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 241 ASN Chi-restraints excluded: chain b residue 577 VAL Chi-restraints excluded: chain b residue 587 THR Chi-restraints excluded: chain b residue 617 CYS Chi-restraints excluded: chain b residue 618 HIS Chi-restraints excluded: chain b residue 913 THR Chi-restraints excluded: chain b residue 923 LEU Chi-restraints excluded: chain b residue 964 THR Chi-restraints excluded: chain d residue 236 SER Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 286 GLU Chi-restraints excluded: chain d residue 460 CYS Chi-restraints excluded: chain d residue 659 ILE Chi-restraints excluded: chain d residue 675 GLU Chi-restraints excluded: chain d residue 766 SER Chi-restraints excluded: chain d residue 845 GLN Chi-restraints excluded: chain d residue 857 LYS Chi-restraints excluded: chain d residue 993 GLN Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1105 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 487 optimal weight: 20.0000 chunk 332 optimal weight: 40.0000 chunk 8 optimal weight: 2.9990 chunk 436 optimal weight: 0.9980 chunk 241 optimal weight: 0.9990 chunk 499 optimal weight: 0.8980 chunk 404 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 525 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN I 18 GLN I 45 GLN I 56 ASN I 98 GLN a 345 ASN b 807 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 790 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 50513 Z= 0.333 Angle : 0.555 10.461 68634 Z= 0.293 Chirality : 0.043 0.177 7644 Planarity : 0.004 0.070 8595 Dihedral : 12.370 175.139 7610 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.28 % Allowed : 12.65 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % 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: -0.39 (0.11), residues: 5954 helix: 1.05 (0.12), residues: 1822 sheet: -0.73 (0.14), residues: 1211 loop : -0.84 (0.11), residues: 2921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 207 HIS 0.008 0.001 HIS a 180 PHE 0.020 0.002 PHE d1097 TYR 0.018 0.001 TYR J 43 ARG 0.008 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 695 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 629 time to evaluate : 5.809 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: A 105 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7565 (mtpt) REVERT: A 343 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.7928 (pp) REVERT: A 893 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: B 394 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7432 (t0) REVERT: B 611 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: E 98 ASN cc_start: 0.7619 (t0) cc_final: 0.7378 (t0) REVERT: a 16 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7777 (tt) REVERT: b 646 ASP cc_start: 0.7465 (t0) cc_final: 0.7073 (t0) REVERT: d 244 LYS cc_start: 0.7707 (tppt) cc_final: 0.7473 (tppt) REVERT: d 581 MET cc_start: 0.7208 (tpp) cc_final: 0.6894 (mmp) REVERT: d 845 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: d 993 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7153 (mp10) REVERT: d 1079 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6971 (pm20) outliers start: 66 outliers final: 36 residues processed: 668 average time/residue: 2.9642 time to fit residues: 2492.7052 Evaluate side-chains 663 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 619 time to evaluate : 5.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 1151 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 241 ASN Chi-restraints excluded: chain b residue 577 VAL Chi-restraints excluded: chain b residue 587 THR Chi-restraints excluded: chain b residue 617 CYS Chi-restraints excluded: chain b residue 618 HIS Chi-restraints excluded: chain b residue 913 THR Chi-restraints excluded: chain b residue 964 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 54 GLU Chi-restraints excluded: chain d residue 236 SER Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 460 CYS Chi-restraints excluded: chain d residue 603 LEU Chi-restraints excluded: chain d residue 638 LEU Chi-restraints excluded: chain d residue 659 ILE Chi-restraints excluded: chain d residue 675 GLU Chi-restraints excluded: chain d residue 766 SER Chi-restraints excluded: chain d residue 845 GLN Chi-restraints excluded: chain d residue 857 LYS Chi-restraints excluded: chain d residue 993 GLN Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1079 GLU Chi-restraints excluded: chain d residue 1105 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 197 optimal weight: 0.0870 chunk 527 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 586 optimal weight: 1.9990 chunk 486 optimal weight: 10.0000 chunk 271 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 193 optimal weight: 0.0970 chunk 307 optimal weight: 0.5980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN C 18 ASN C 111 GLN C 232 ASN I 18 GLN a 345 ASN d 372 GLN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 50513 Z= 0.147 Angle : 0.501 9.090 68634 Z= 0.263 Chirality : 0.041 0.174 7644 Planarity : 0.004 0.079 8595 Dihedral : 12.205 177.252 7610 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.83 % Allowed : 13.38 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 5954 helix: 1.35 (0.13), residues: 1819 sheet: -0.70 (0.14), residues: 1222 loop : -0.72 (0.11), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 207 HIS 0.005 0.001 HIS C 66 PHE 0.014 0.001 PHE d1030 TYR 0.013 0.001 TYR J 43 ARG 0.010 0.000 ARG A 928 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 688 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 645 time to evaluate : 5.823 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: A 105 LYS cc_start: 0.7764 (mtpt) cc_final: 0.7464 (mtpt) REVERT: A 343 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7809 (pp) REVERT: E 98 ASN cc_start: 0.7576 (t0) cc_final: 0.7322 (t0) REVERT: a 16 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7702 (tt) REVERT: b 646 ASP cc_start: 0.7443 (t0) cc_final: 0.7096 (t0) REVERT: b 868 LEU cc_start: 0.8007 (tt) cc_final: 0.7788 (tp) REVERT: d 581 MET cc_start: 0.7212 (tpp) cc_final: 0.6970 (mmp) REVERT: d 593 MET cc_start: 0.7069 (mtp) cc_final: 0.6747 (mtp) outliers start: 43 outliers final: 27 residues processed: 667 average time/residue: 2.9928 time to fit residues: 2532.1707 Evaluate side-chains 641 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 612 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 241 ASN Chi-restraints excluded: chain b residue 577 VAL Chi-restraints excluded: chain b residue 587 THR Chi-restraints excluded: chain b residue 913 THR Chi-restraints excluded: chain b residue 964 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 286 GLU Chi-restraints excluded: chain d residue 460 CYS Chi-restraints excluded: chain d residue 603 LEU Chi-restraints excluded: chain d residue 638 LEU Chi-restraints excluded: chain d residue 659 ILE Chi-restraints excluded: chain d residue 675 GLU Chi-restraints excluded: chain d residue 857 LYS Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1105 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 565 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 334 optimal weight: 50.0000 chunk 428 optimal weight: 0.0970 chunk 331 optimal weight: 40.0000 chunk 493 optimal weight: 1.9990 chunk 327 optimal weight: 6.9990 chunk 584 optimal weight: 1.9990 chunk 365 optimal weight: 0.8980 chunk 356 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 56 ASN d 149 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 978 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 50513 Z= 0.306 Angle : 0.536 10.333 68634 Z= 0.282 Chirality : 0.042 0.169 7644 Planarity : 0.004 0.078 8595 Dihedral : 12.212 174.558 7610 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.06 % Allowed : 13.65 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5954 helix: 1.32 (0.13), residues: 1826 sheet: -0.64 (0.14), residues: 1202 loop : -0.71 (0.11), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP d 207 HIS 0.006 0.001 HIS a 180 PHE 0.029 0.002 PHE d1097 TYR 0.017 0.001 TYR J 43 ARG 0.010 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 685 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 630 time to evaluate : 5.933 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: A 105 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7497 (mtpt) REVERT: A 343 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7834 (pp) REVERT: B 394 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7351 (t0) REVERT: B 436 LYS cc_start: 0.8516 (ptmt) cc_final: 0.8284 (ptmm) REVERT: E 98 ASN cc_start: 0.7601 (t0) cc_final: 0.7355 (t0) REVERT: a 16 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7761 (tt) REVERT: b 646 ASP cc_start: 0.7546 (t0) cc_final: 0.7159 (t0) REVERT: d 581 MET cc_start: 0.7244 (tpp) cc_final: 0.6956 (mmp) REVERT: d 993 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7148 (mp10) outliers start: 55 outliers final: 34 residues processed: 663 average time/residue: 3.0028 time to fit residues: 2523.0863 Evaluate side-chains 653 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 615 time to evaluate : 5.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 241 ASN Chi-restraints excluded: chain b residue 577 VAL Chi-restraints excluded: chain b residue 587 THR Chi-restraints excluded: chain b residue 617 CYS Chi-restraints excluded: chain b residue 913 THR Chi-restraints excluded: chain b residue 964 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 286 GLU Chi-restraints excluded: chain d residue 367 LEU Chi-restraints excluded: chain d residue 460 CYS Chi-restraints excluded: chain d residue 603 LEU Chi-restraints excluded: chain d residue 638 LEU Chi-restraints excluded: chain d residue 659 ILE Chi-restraints excluded: chain d residue 675 GLU Chi-restraints excluded: chain d residue 857 LYS Chi-restraints excluded: chain d residue 993 GLN Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1105 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 361 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 348 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 397 optimal weight: 0.9980 chunk 288 optimal weight: 40.0000 chunk 54 optimal weight: 0.4980 chunk 459 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 232 ASN I 18 GLN a 345 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 50513 Z= 0.188 Angle : 0.507 9.089 68634 Z= 0.266 Chirality : 0.041 0.167 7644 Planarity : 0.004 0.093 8595 Dihedral : 12.151 175.503 7610 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.01 % Allowed : 14.17 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.11), residues: 5954 helix: 1.46 (0.13), residues: 1826 sheet: -0.60 (0.14), residues: 1207 loop : -0.67 (0.11), residues: 2921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 589 HIS 0.005 0.001 HIS d 578 PHE 0.020 0.001 PHE G 44 TYR 0.014 0.001 TYR J 43 ARG 0.014 0.000 ARG a 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 693 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 641 time to evaluate : 6.747 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: A 105 LYS cc_start: 0.7783 (mtpt) cc_final: 0.7481 (mtpt) REVERT: A 343 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7770 (pp) REVERT: A 893 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: B 394 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7315 (t0) REVERT: B 436 LYS cc_start: 0.8500 (ptmt) cc_final: 0.8286 (ptmm) REVERT: E 98 ASN cc_start: 0.7581 (t0) cc_final: 0.7328 (t0) REVERT: K 24 ASP cc_start: 0.7851 (t0) cc_final: 0.7582 (t70) REVERT: a 16 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7703 (tt) REVERT: b 646 ASP cc_start: 0.7532 (t0) cc_final: 0.7158 (t0) REVERT: d 581 MET cc_start: 0.7306 (tpp) cc_final: 0.7031 (mmp) outliers start: 52 outliers final: 36 residues processed: 674 average time/residue: 2.9768 time to fit residues: 2544.2569 Evaluate side-chains 661 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 621 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 548 TRP Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 241 ASN Chi-restraints excluded: chain b residue 577 VAL Chi-restraints excluded: chain b residue 587 THR Chi-restraints excluded: chain b residue 617 CYS Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 913 THR Chi-restraints excluded: chain b residue 964 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 460 CYS Chi-restraints excluded: chain d residue 603 LEU Chi-restraints excluded: chain d residue 659 ILE Chi-restraints excluded: chain d residue 675 GLU Chi-restraints excluded: chain d residue 790 ASN Chi-restraints excluded: chain d residue 857 LYS Chi-restraints excluded: chain d residue 930 VAL Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1105 MET Chi-restraints excluded: chain d residue 1129 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 531 optimal weight: 0.0170 chunk 559 optimal weight: 10.0000 chunk 510 optimal weight: 1.9990 chunk 544 optimal weight: 0.8980 chunk 327 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 427 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 491 optimal weight: 50.0000 chunk 514 optimal weight: 0.5980 chunk 542 optimal weight: 0.3980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1101 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 518 HIS B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN E 168 ASN I 18 GLN I 56 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50513 Z= 0.193 Angle : 0.509 9.398 68634 Z= 0.266 Chirality : 0.041 0.272 7644 Planarity : 0.004 0.092 8595 Dihedral : 12.098 175.192 7610 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.95 % Allowed : 14.40 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.11), residues: 5954 helix: 1.55 (0.13), residues: 1827 sheet: -0.55 (0.15), residues: 1207 loop : -0.63 (0.12), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 589 HIS 0.004 0.001 HIS A 947 PHE 0.033 0.001 PHE d1097 TYR 0.014 0.001 TYR J 43 ARG 0.012 0.000 ARG a 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 686 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 637 time to evaluate : 5.833 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: A 343 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7754 (pp) REVERT: A 893 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: A 1149 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7430 (mtm-85) REVERT: B 394 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7339 (t0) REVERT: B 436 LYS cc_start: 0.8502 (ptmt) cc_final: 0.8297 (ptmm) REVERT: E 98 ASN cc_start: 0.7578 (t0) cc_final: 0.7322 (t0) REVERT: a 16 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7701 (tt) REVERT: b 646 ASP cc_start: 0.7552 (t0) cc_final: 0.7170 (t0) REVERT: d 581 MET cc_start: 0.7281 (tpp) cc_final: 0.7040 (mmp) outliers start: 49 outliers final: 32 residues processed: 664 average time/residue: 2.9936 time to fit residues: 2522.6717 Evaluate side-chains 659 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 623 time to evaluate : 5.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 241 ASN Chi-restraints excluded: chain b residue 577 VAL Chi-restraints excluded: chain b residue 587 THR Chi-restraints excluded: chain b residue 617 CYS Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 913 THR Chi-restraints excluded: chain b residue 964 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 460 CYS Chi-restraints excluded: chain d residue 603 LEU Chi-restraints excluded: chain d residue 638 LEU Chi-restraints excluded: chain d residue 659 ILE Chi-restraints excluded: chain d residue 675 GLU Chi-restraints excluded: chain d residue 857 LYS Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 357 optimal weight: 0.9990 chunk 575 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 400 optimal weight: 0.8980 chunk 603 optimal weight: 4.9990 chunk 555 optimal weight: 8.9990 chunk 480 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 371 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 518 HIS B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN E 168 ASN I 18 GLN I 56 ASN a 345 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 50513 Z= 0.240 Angle : 0.520 9.740 68634 Z= 0.272 Chirality : 0.042 0.175 7644 Planarity : 0.004 0.094 8595 Dihedral : 12.104 174.234 7610 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.89 % Allowed : 14.66 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.11), residues: 5954 helix: 1.54 (0.13), residues: 1827 sheet: -0.56 (0.14), residues: 1219 loop : -0.62 (0.12), residues: 2908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 589 HIS 0.005 0.001 HIS a 180 PHE 0.037 0.001 PHE d1097 TYR 0.016 0.001 TYR J 43 ARG 0.013 0.000 ARG a 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11908 Ramachandran restraints generated. 5954 Oldfield, 0 Emsley, 5954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 335 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue LYS 7 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue VAL 9 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 13 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue SER 15 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 25 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue SER 40 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ALA 48 is missing expected H atoms. Skipping. Residue LEU 50 is missing expected H atoms. Skipping. Residue THR 51 is missing expected H atoms. Skipping. Residue ALA 55 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue ALA 61 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 65 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue SER 72 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue VAL 79 is missing expected H atoms. Skipping. Residue VAL 80 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue THR 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ALA 96 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue ALA 105 is missing expected H atoms. Skipping. Residue ALA 106 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue LYS 123 is missing expected H atoms. Skipping. Residue ALA 127 is missing expected H atoms. Skipping. Residue TYR 128 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue LEU 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue LEU 133 is missing expected H atoms. Skipping. Residue TYR 135 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue LYS 142 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 150 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 298 is missing expected H atoms. Skipping. Residue MET 437 is missing expected H atoms. Skipping. Residue LYS 484 is missing expected H atoms. Skipping. Residue LYS 491 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Residue LYS 570 is missing expected H atoms. Skipping. Residue LYS 579 is missing expected H atoms. Skipping. Residue LYS 665 is missing expected H atoms. Skipping. Residue LYS 674 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 820 is missing expected H atoms. Skipping. Residue LYS 823 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue LYS 857 is missing expected H atoms. Skipping. Residue LYS 897 is missing expected H atoms. Skipping. Residue MET 938 is missing expected H atoms. Skipping. Residue LYS 979 is missing expected H atoms. Skipping. Residue LYS 1104 is missing expected H atoms. Skipping. Residue LYS 1131 is missing expected H atoms. Skipping. Evaluate side-chains 681 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 635 time to evaluate : 5.981 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: A 343 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7756 (pp) REVERT: A 1149 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7357 (mtm-85) REVERT: B 254 GLN cc_start: 0.7604 (mt0) cc_final: 0.7200 (mt0) REVERT: B 394 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7366 (t0) REVERT: E 98 ASN cc_start: 0.7638 (t0) cc_final: 0.7371 (t0) REVERT: a 16 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7707 (tt) REVERT: b 646 ASP cc_start: 0.7565 (t0) cc_final: 0.7202 (t0) REVERT: d 581 MET cc_start: 0.7351 (tpp) cc_final: 0.7096 (mmp) outliers start: 46 outliers final: 34 residues processed: 659 average time/residue: 2.9840 time to fit residues: 2492.1309 Evaluate side-chains 656 residues out of total 5324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 619 time to evaluate : 5.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 1285 LEU Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 209 SER Chi-restraints excluded: chain a residue 241 ASN Chi-restraints excluded: chain b residue 577 VAL Chi-restraints excluded: chain b residue 587 THR Chi-restraints excluded: chain b residue 617 CYS Chi-restraints excluded: chain b residue 618 HIS Chi-restraints excluded: chain b residue 806 CYS Chi-restraints excluded: chain b residue 913 THR Chi-restraints excluded: chain b residue 964 THR Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 218 MET Chi-restraints excluded: chain d residue 255 GLN Chi-restraints excluded: chain d residue 460 CYS Chi-restraints excluded: chain d residue 603 LEU Chi-restraints excluded: chain d residue 638 LEU Chi-restraints excluded: chain d residue 659 ILE Chi-restraints excluded: chain d residue 675 GLU Chi-restraints excluded: chain d residue 790 ASN Chi-restraints excluded: chain d residue 857 LYS Chi-restraints excluded: chain d residue 1036 MET Chi-restraints excluded: chain d residue 1105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 381 optimal weight: 0.3980 chunk 512 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 443 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 481 optimal weight: 9.9990 chunk 201 optimal weight: 0.4980 chunk 494 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN A1101 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 518 HIS B 654 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN E 168 ASN I 18 GLN I 56 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.162765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.102666 restraints weight = 174450.168| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.52 r_work: 0.2952 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 50513 Z= 0.304 Angle : 0.543 10.133 68634 Z= 0.285 Chirality : 0.042 0.175 7644 Planarity : 0.004 0.104 8595 Dihedral : 12.149 173.761 7610 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.02 % Allowed : 14.69 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.11), residues: 5954 helix: 1.50 (0.13), residues: 1821 sheet: -0.60 (0.14), residues: 1230 loop : -0.62 (0.12), residues: 2903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 589 HIS 0.006 0.001 HIS a 180 PHE 0.041 0.002 PHE d1097 TYR 0.018 0.001 TYR J 43 ARG 0.013 0.001 ARG A 928 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36270.32 seconds wall clock time: 623 minutes 55.58 seconds (37435.58 seconds total)