Starting phenix.real_space_refine on Tue Mar 19 01:27:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oob_13009/03_2024/7oob_13009_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oob_13009/03_2024/7oob_13009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oob_13009/03_2024/7oob_13009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oob_13009/03_2024/7oob_13009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oob_13009/03_2024/7oob_13009_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oob_13009/03_2024/7oob_13009_trim_updated.pdb" } resolution = 2.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 10 Type Number sf(0) Gaussians Zn 8 6.06 5 P 94 5.49 5 Mg 2 5.21 5 S 269 5.16 5 Be 1 3.05 5 C 28954 2.51 5 N 8082 2.21 5 O 8848 1.98 5 F 3 1.80 5 H 44484 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 "b ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 705": "OE1" <-> "OE2" Residue "b GLU 792": "OE1" <-> "OE2" 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 ARG 950": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 985": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d GLU 65": "OE1" <-> "OE2" Residue "d GLU 72": "OE1" <-> "OE2" Residue "d GLU 127": "OE1" <-> "OE2" Residue "d GLU 199": "OE1" <-> "OE2" Residue "d GLU 351": "OE1" <-> "OE2" Residue "d GLU 842": "OE1" <-> "OE2" Residue "d GLU 863": "OE1" <-> "OE2" Residue "d GLU 875": "OE1" <-> "OE2" Residue "d GLU 898": "OE1" <-> "OE2" Residue "d PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 1045": "OE1" <-> "OE2" Residue "a GLU 13": "OE1" <-> "OE2" Residue "a GLU 39": "OE1" <-> "OE2" Residue "a GLU 238": "OE1" <-> "OE2" Residue "a GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 90745 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 22494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 22494 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: 4120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 4120 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: "b" Number of atoms: 8561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 8561 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 21, 'TRANS': 498} Chain breaks: 3 Chain: "d" Number of atoms: 12317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 12317 Classifications: {'peptide': 781} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 754} Chain breaks: 7 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: 5626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5626 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 355} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 942 SG CYS A 71 44.516 82.987 104.483 1.00 35.35 S ATOM 983 SG CYS A 74 44.670 86.585 104.248 1.00 32.47 S ATOM 1070 SG CYS A 81 45.669 85.135 101.437 1.00 28.37 S ATOM 1553 SG CYS A 111 89.282 77.762 119.122 1.00 73.15 S ATOM 2263 SG CYS A 154 91.437 79.792 120.774 1.00 84.57 S ATOM 2301 SG CYS A 184 91.175 76.229 122.300 1.00 81.11 S ATOM 39753 SG CYS B1119 56.195 95.094 112.525 1.00 27.09 S ATOM 39796 SG CYS B1122 58.516 92.441 111.347 1.00 24.13 S ATOM 40021 SG CYS B1137 55.347 91.298 112.007 1.00 39.03 S ATOM 40062 SG CYS B1140 58.207 93.062 114.606 1.00 44.36 S ATOM 42015 SG CYS C 88 13.310 97.631 45.108 1.00 26.32 S ATOM 42039 SG CYS C 90 13.068 94.984 47.285 1.00 37.75 S ATOM 42099 SG CYS C 94 12.329 94.943 44.221 1.00 19.82 S ATOM 42138 SG CYS C 97 16.144 95.025 44.583 1.00 15.27 S ATOM 56773 SG CYS I 17 121.833 44.887 72.891 1.00 62.49 S ATOM 56815 SG CYS I 20 118.787 45.240 74.775 1.00 61.01 S ATOM 57136 SG CYS I 39 120.111 47.678 76.108 1.00 69.82 S ATOM 57184 SG CYS I 42 122.091 44.655 75.879 1.00 73.48 S ATOM 57857 SG CYS I 86 113.668 63.735 33.360 1.00 33.22 S ATOM 57906 SG CYS I 89 112.591 61.339 31.227 1.00 39.04 S ATOM 58298 SG CYS I 114 110.057 62.261 32.885 1.00 27.04 S ATOM 58363 SG CYS I 119 112.889 59.955 34.174 1.00 41.38 S ATOM 58585 SG CYS J 7 44.203 89.624 32.368 1.00 11.32 S ATOM 58629 SG CYS J 10 42.337 92.042 30.405 1.00 11.32 S ATOM 59154 SG CYS J 44 46.193 91.666 30.167 1.00 11.32 S ATOM 59164 SG CYS J 45 43.816 89.541 28.507 1.00 11.32 S ATOM 61528 SG CYS L 19 32.107 54.102 55.197 1.00 41.38 S ATOM 61560 SG CYS L 22 29.787 52.568 53.501 1.00 49.28 S ATOM 61790 SG CYS L 36 29.082 52.209 56.625 1.00 48.37 S ATOM 61839 SG CYS L 39 32.437 50.518 54.911 1.00 52.17 S Time building chain proxies: 29.18, per 1000 atoms: 0.32 Number of scatterers: 90745 At special positions: 0 Unit cell: (156.45, 172.2, 225.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 8 29.99 S 269 16.00 P 94 15.00 Mg 2 11.99 F 3 9.00 O 8848 8.00 N 8082 7.00 C 28954 6.00 Be 1 4.00 H 44484 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: 57.74 Conformation dependent library (CDL) restraints added in 6.5 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 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " 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 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10410 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 65 sheets defined 28.8% alpha, 18.2% beta 39 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 37.39 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.533A pdb=" N LEU A 100 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL A 101 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.742A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 275 through 295 Processing helix chain 'A' and resid 300 through 318 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 557 through 566 removed outlier: 4.001A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.752A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 662 through 683 removed outlier: 3.990A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 833 through 868 removed outlier: 4.170A 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 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 Processing helix chain 'A' and resid 947 through 969 Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1019 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1053 through 1056 No H-bonds generated for 'chain 'A' and resid 1053 through 1056' Processing helix chain 'A' and resid 1062 through 1078 Processing helix chain 'A' and resid 1087 through 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1121 through 1128 Processing helix chain 'A' and resid 1146 through 1148 No H-bonds generated for 'chain 'A' and resid 1146 through 1148' Processing helix chain 'A' and resid 1151 through 1161 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 1190 through 1197 Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1228 through 1238 Processing helix chain 'A' and resid 1281 through 1295 removed outlier: 4.000A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1346 No H-bonds generated for 'chain 'A' and resid 1343 through 1346' Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1371 through 1387 Processing helix chain 'A' and resid 1395 through 1404 Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1432 removed outlier: 3.588A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1445 Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'B' and resid 19 through 36 removed outlier: 4.946A pdb=" N GLN B 23 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS B 26 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 295 through 307 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 358 through 376 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 396 through 425 removed outlier: 3.569A pdb=" N PHE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 547 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 592 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 679 through 682 Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 728 Processing helix chain 'B' and resid 764 through 767 No H-bonds generated for 'chain 'B' and resid 764 through 767' Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 971 No H-bonds generated for 'chain 'B' and resid 969 through 971' Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.530A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1057 No H-bonds generated for 'chain 'B' and resid 1055 through 1057' Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1153 through 1165 removed outlier: 3.561A pdb=" N MET B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.588A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 269 Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 70 Processing helix chain 'D' and resid 78 through 89 Processing helix chain 'D' and resid 94 through 103 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 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 136 Processing helix chain 'E' and resid 4 through 24 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 44 Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 132 through 135 No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 23 through 34 Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'H' and resid 129 through 131 No H-bonds generated for 'chain 'H' and resid 129 through 131' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.879A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.552A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 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 83 through 114 Processing helix chain 'b' and resid 501 through 505 Processing helix chain 'b' and resid 509 through 524 Processing helix chain 'b' and resid 539 through 551 Processing helix chain 'b' and resid 578 through 588 Processing helix chain 'b' and resid 607 through 617 Processing helix chain 'b' and resid 625 through 630 Processing helix chain 'b' and resid 632 through 635 No H-bonds generated for 'chain 'b' and resid 632 through 635' Processing helix chain 'b' and resid 648 through 651 Processing helix chain 'b' and resid 657 through 664 removed outlier: 3.605A pdb=" N GLN b 664 " --> pdb=" O LEU b 660 " (cutoff:3.500A) Processing helix chain 'b' and resid 682 through 692 Processing helix chain 'b' and resid 700 through 713 removed outlier: 4.816A 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 721 through 738 Processing helix chain 'b' and resid 751 through 753 No H-bonds generated for 'chain 'b' and resid 751 through 753' Processing helix chain 'b' and resid 770 through 780 Processing helix chain 'b' and resid 783 through 789 Processing helix chain 'b' and resid 795 through 807 Processing helix chain 'b' and resid 835 through 837 No H-bonds generated for 'chain 'b' and resid 835 through 837' Processing helix chain 'b' and resid 839 through 853 Processing helix chain 'b' and resid 865 through 877 Processing helix chain 'b' and resid 891 through 903 removed outlier: 4.941A pdb=" N GLN b 895 " --> pdb=" O ALA b 892 " (cutoff:3.500A) Proline residue: b 896 - end of helix Processing helix chain 'b' and resid 914 through 917 No H-bonds generated for 'chain 'b' and resid 914 through 917' Processing helix chain 'b' and resid 938 through 947 Processing helix chain 'b' and resid 968 through 987 removed outlier: 4.031A pdb=" N VAL b 986 " --> pdb=" O LEU b 982 " (cutoff:3.500A) Processing helix chain 'b' and resid 1388 through 1398 Processing helix chain 'd' and resid 251 through 253 No H-bonds generated for 'chain 'd' and resid 251 through 253' Processing helix chain 'd' and resid 367 through 369 No H-bonds generated for 'chain 'd' and resid 367 through 369' Processing helix chain 'd' and resid 728 through 730 No H-bonds generated for 'chain 'd' and resid 728 through 730' Processing helix chain 'd' and resid 987 through 990 Processing helix chain 'd' and resid 1045 through 1061 Processing helix chain 'd' and resid 1070 through 1074 Processing helix chain 'd' and resid 1091 through 1098 removed outlier: 3.735A pdb=" N PHE d1097 " --> pdb=" O LEU d1093 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU d1098 " --> pdb=" O ILE d1094 " (cutoff:3.500A) Processing helix chain 'd' and resid 1102 through 1108 Processing helix chain 'd' and resid 1126 through 1139 removed outlier: 4.283A pdb=" N ILE d1139 " --> pdb=" O GLU d1135 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 9 Processing helix chain 'a' and resid 15 through 28 Processing sheet with id= A, first strand: chain 'A' and resid 86 through 89 Processing sheet with id= B, 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= C, first strand: chain 'A' and resid 362 through 366 Processing sheet with id= D, first strand: chain 'A' and resid 367 through 369 removed outlier: 6.143A pdb=" N PHE A 482 " --> pdb=" O THR A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 389 through 393 Processing sheet with id= F, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= G, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= H, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id= I, 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: 7.001A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id= K, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.709A 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= L, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= M, first strand: chain 'B' and resid 140 through 144 removed outlier: 4.123A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= O, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= P, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.657A 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= Q, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= R, first strand: chain 'B' and resid 530 through 532 Processing sheet with id= S, first strand: chain 'B' and resid 602 through 605 removed outlier: 3.574A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 747 through 751 removed outlier: 5.649A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 1042 through 1048 removed outlier: 4.164A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 965 " --> pdb=" O ALA B 781 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 794 " --> pdb=" O LYS B 942 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR B 944 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N MET B 796 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY B 946 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 827 through 829 Processing sheet with id= W, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id= X, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id= Y, first strand: chain 'B' and resid 121 through 126 removed outlier: 6.137A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 182 through 185 removed outlier: 6.718A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 99 through 106 removed outlier: 6.124A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 113 through 116 Processing sheet with id= AC, 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: 6.721A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 147 through 150 removed outlier: 7.701A pdb=" N GLN E 210 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AF, first strand: chain 'G' and resid 5 through 13 removed outlier: 3.589A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 104 through 109 removed outlier: 5.825A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.812A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.675A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 5.108A 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: 6.532A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 25 through 29 Processing sheet with id= AK, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= AL, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AM, first strand: chain 'L' and resid 25 through 27 Processing sheet with id= AN, first strand: chain 'b' and resid 528 through 530 Processing sheet with id= AO, first strand: chain 'b' and resid 569 through 572 Processing sheet with id= AP, first strand: chain 'b' and resid 759 through 766 removed outlier: 6.785A pdb=" N VAL b 957 " --> pdb=" O ASN b 760 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLN b 762 " --> pdb=" O VAL b 957 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL b 959 " --> pdb=" O GLN b 762 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU b 764 " --> pdb=" O VAL b 959 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG b 961 " --> pdb=" O LEU b 764 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS b 766 " --> pdb=" O ARG b 961 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU b 963 " --> pdb=" O CYS b 766 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'd' and resid 1088 through 1090 removed outlier: 6.919A pdb=" N ASN d 4 " --> pdb=" O ILE d1089 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE d1037 " --> pdb=" O ALA d 9 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL d1006 " --> pdb=" O GLY d1031 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'd' and resid 17 through 21 removed outlier: 6.078A pdb=" N VAL d 43 " --> pdb=" O PRO d 51 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'd' and resid 61 through 67 removed outlier: 6.490A pdb=" N LEU d 80 " --> pdb=" O ALA d 62 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET d 64 " --> pdb=" O PHE d 78 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE d 78 " --> pdb=" O MET d 64 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU d 66 " --> pdb=" O LEU d 76 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU d 76 " --> pdb=" O LEU d 66 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU d 90 " --> pdb=" O THR d 102 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR d 102 " --> pdb=" O GLU d 90 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS d 92 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE d 100 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER d 94 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE d 98 " --> pdb=" O SER d 94 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'd' and resid 121 through 124 Processing sheet with id= AU, first strand: chain 'd' and resid 201 through 204 removed outlier: 3.615A pdb=" N ASP d 166 " --> pdb=" O VAL d 181 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN d 183 " --> pdb=" O VAL d 164 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL d 164 " --> pdb=" O GLN d 183 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'd' and resid 218 through 221 Processing sheet with id= AW, first strand: chain 'd' and resid 258 through 263 removed outlier: 6.669A pdb=" N GLY d 274 " --> pdb=" O VAL d 259 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N HIS d 261 " --> pdb=" O LEU d 272 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU d 272 " --> pdb=" O HIS d 261 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG d 263 " --> pdb=" O ARG d 270 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG d 270 " --> pdb=" O ARG d 263 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET d 282 " --> pdb=" O LEU d 304 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU d 304 " --> pdb=" O MET d 282 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU d 284 " --> pdb=" O VAL d 302 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL d 302 " --> pdb=" O LEU d 284 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU d 286 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU d 300 " --> pdb=" O GLU d 286 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'd' and resid 313 through 318 removed outlier: 6.677A pdb=" N VAL d 321 " --> pdb=" O LEU d 317 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS d 335 " --> pdb=" O ALA d 349 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA d 349 " --> pdb=" O LYS d 335 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'd' and resid 361 through 364 removed outlier: 4.051A pdb=" N ASP d 361 " --> pdb=" O CYS d 378 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.482A pdb=" N LEU d 736 " --> pdb=" O ARG d 722 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE d 724 " --> pdb=" O GLY d 734 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY d 734 " --> pdb=" O ILE d 724 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR d 726 " --> pdb=" O CYS d 732 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N CYS d 732 " --> pdb=" O TYR d 726 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP d 795 " --> pdb=" O VAL d 801 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL d 801 " --> pdb=" O ASP d 795 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER d 764 " --> pdb=" O GLN d 806 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'd' and resid 811 through 819 removed outlier: 6.565A pdb=" N GLY d 832 " --> pdb=" O LEU d 814 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU d 816 " --> pdb=" O ILE d 830 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE d 830 " --> pdb=" O LEU d 816 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER d 818 " --> pdb=" O TYR d 828 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR d 828 " --> pdb=" O SER d 818 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN d 852 " --> pdb=" O THR d 860 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR d 860 " --> pdb=" O GLN d 852 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER d 854 " --> pdb=" O LEU d 858 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU d 858 " --> pdb=" O SER d 854 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'd' and resid 873 through 876 removed outlier: 3.572A pdb=" N CYS d 903 " --> pdb=" O LEU d 890 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLU d 892 " --> pdb=" O THR d 901 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR d 901 " --> pdb=" O GLU d 892 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'd' and resid 911 through 917 removed outlier: 6.548A pdb=" N GLY d 924 " --> pdb=" O LEU d 912 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU d 914 " --> pdb=" O LEU d 922 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU d 922 " --> pdb=" O LEU d 914 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR d 916 " --> pdb=" O PHE d 920 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N PHE d 920 " --> pdb=" O THR d 916 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA d 934 " --> pdb=" O GLU d 944 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU d 944 " --> pdb=" O ALA d 934 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS d 936 " --> pdb=" O PHE d 942 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE d 942 " --> pdb=" O LYS d 936 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'd' and resid 954 through 959 removed outlier: 6.770A pdb=" N ALA d 968 " --> pdb=" O SER d 955 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL d 957 " --> pdb=" O LEU d 966 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU d 966 " --> pdb=" O VAL d 957 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE d 959 " --> pdb=" O ASN d 964 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN d 964 " --> pdb=" O ILE d 959 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN d 973 " --> pdb=" O GLU d 969 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN d 978 " --> pdb=" O GLU d 994 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU d 994 " --> pdb=" O GLN d 978 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'd' and resid 1076 through 1078 Processing sheet with id= BF, first strand: chain 'a' and resid 30 through 32 removed outlier: 3.625A pdb=" N CYS a 339 " --> pdb=" O GLY a 352 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'a' and resid 36 through 38 removed outlier: 6.502A pdb=" N TYR a 82 " --> pdb=" O ASP a 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.751A pdb=" N GLY a 62 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU a 49 " --> pdb=" O LEU a 60 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU a 60 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE a 51 " --> pdb=" O TYR a 58 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR a 58 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP a 72 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA a 86 " --> pdb=" O ASP a 72 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 102 through 107 removed outlier: 6.777A pdb=" N SER a 118 " --> pdb=" O GLU a 103 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL a 105 " --> pdb=" O THR a 116 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR a 116 " --> pdb=" O VAL a 105 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TRP a 107 " --> pdb=" O MET a 114 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N MET a 114 " --> pdb=" O TRP a 107 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASP a 128 " --> pdb=" O THR a 134 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR a 134 " --> pdb=" O ASP a 128 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'a' and resid 169 through 172 Processing sheet with id= BK, first strand: chain 'a' and resid 211 through 215 Processing sheet with id= BL, first strand: chain 'a' and resid 268 through 273 removed outlier: 3.555A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'a' and resid 307 through 312 removed outlier: 6.300A pdb=" N THR a 320 " --> pdb=" O GLN a 326 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN a 326 " --> pdb=" O THR a 320 " (cutoff:3.500A) 1470 hydrogen bonds defined for protein. 4116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 36.41 Time building geometry restraints manager: 60.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 44396 1.03 - 1.22: 128 1.22 - 1.42: 19641 1.42 - 1.62: 27236 1.62 - 1.81: 420 Bond restraints: 91821 Sorted by residual: bond pdb=" BE BEF b1502 " pdb=" F2 BEF b1502 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" BE BEF b1502 " pdb=" F3 BEF b1502 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" CA ASN A1129 " pdb=" CB ASN A1129 " ideal model delta sigma weight residual 1.525 1.568 -0.042 1.29e-02 6.01e+03 1.08e+01 bond pdb=" BE BEF b1502 " pdb=" F1 BEF b1502 " ideal model delta sigma weight residual 1.476 1.533 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" CA GLU C 210 " pdb=" CB GLU C 210 " ideal model delta sigma weight residual 1.531 1.604 -0.073 3.12e-02 1.03e+03 5.52e+00 ... (remaining 91816 not shown) Histogram of bond angle deviations from ideal: 53.52 - 70.83: 26 70.83 - 88.13: 18 88.13 - 105.43: 1314 105.43 - 122.73: 152379 122.73 - 140.03: 11883 Bond angle restraints: 165620 Sorted by residual: angle pdb=" HZ1 LYS A1014 " pdb=" NZ LYS A1014 " pdb=" HZ2 LYS A1014 " ideal model delta sigma weight residual 109.00 53.52 55.48 3.00e+00 1.11e-01 3.42e+02 angle pdb=" HZ1 LYS I 57 " pdb=" NZ LYS I 57 " pdb=" HZ2 LYS I 57 " ideal model delta sigma weight residual 109.00 54.24 54.76 3.00e+00 1.11e-01 3.33e+02 angle pdb=" HZ1 LYS A 874 " pdb=" NZ LYS A 874 " pdb=" HZ2 LYS A 874 " ideal model delta sigma weight residual 109.00 54.85 54.15 3.00e+00 1.11e-01 3.26e+02 angle pdb=" HZ1 LYS B 847 " pdb=" NZ LYS B 847 " pdb=" HZ2 LYS B 847 " ideal model delta sigma weight residual 109.00 55.52 53.48 3.00e+00 1.11e-01 3.18e+02 angle pdb=" HZ1 LYS K 23 " pdb=" NZ LYS K 23 " pdb=" HZ2 LYS K 23 " ideal model delta sigma weight residual 109.00 55.84 53.16 3.00e+00 1.11e-01 3.14e+02 ... (remaining 165615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 41664 35.99 - 71.98: 1239 71.98 - 107.97: 43 107.97 - 143.96: 2 143.96 - 179.95: 7 Dihedral angle restraints: 42955 sinusoidal: 24268 harmonic: 18687 Sorted by residual: 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 -141.00 -39.00 0 5.00e+00 4.00e-02 6.09e+01 dihedral pdb=" O1B ADP b1501 " pdb=" O3A ADP b1501 " pdb=" PB ADP b1501 " pdb=" PA ADP b1501 " ideal model delta sinusoidal sigma weight residual 300.00 139.58 160.41 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' ADP b1501 " pdb=" O5' ADP b1501 " pdb=" PA ADP b1501 " pdb=" O2A ADP b1501 " ideal model delta sinusoidal sigma weight residual 300.00 156.73 143.27 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 42952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4936 0.043 - 0.085: 1635 0.085 - 0.128: 526 0.128 - 0.171: 91 0.171 - 0.214: 8 Chirality restraints: 7196 Sorted by residual: chirality pdb=" CA TYR A 413 " pdb=" N TYR A 413 " pdb=" C TYR A 413 " pdb=" CB TYR A 413 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL A1169 " pdb=" CA VAL A1169 " pdb=" CG1 VAL A1169 " pdb=" CG2 VAL A1169 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB THR b 587 " pdb=" CA THR b 587 " pdb=" OG1 THR b 587 " pdb=" CG2 THR b 587 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 7193 not shown) Planarity restraints: 13272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER d 929 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C SER d 929 " -0.062 2.00e-02 2.50e+03 pdb=" O SER d 929 " 0.022 2.00e-02 2.50e+03 pdb=" N VAL d 930 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN d 759 " 0.015 2.00e-02 2.50e+03 2.47e-02 9.15e+00 pdb=" CD GLN d 759 " -0.053 2.00e-02 2.50e+03 pdb=" OE1 GLN d 759 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 GLN d 759 " 0.015 2.00e-02 2.50e+03 pdb="HE21 GLN d 759 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN d 759 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 334 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO A 335 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.041 5.00e-02 4.00e+02 ... (remaining 13269 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 339 1.84 - 2.53: 77962 2.53 - 3.22: 286761 3.22 - 3.91: 383643 3.91 - 4.60: 606729 Nonbonded interactions: 1355434 Sorted by model distance: nonbonded pdb=" HG1 THR B 565 " pdb=" O ARG B 610 " model vdw 1.146 1.850 nonbonded pdb=" HG SER A 338 " pdb=" OE1 GLN A 341 " model vdw 1.192 1.850 nonbonded pdb=" O LEU A1166 " pdb=" HG1 THR A1170 " model vdw 1.308 1.850 nonbonded pdb=" HZ3 LYS B 847 " pdb=" OD2 ASP B 864 " model vdw 1.347 1.850 nonbonded pdb=" OE2 GLU B 198 " pdb=" HH TYR B 388 " model vdw 1.385 1.850 ... (remaining 1355429 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.970 Extract box with map and model: 15.610 Check model and map are aligned: 0.980 Set scattering table: 0.620 Process input model: 270.960 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.200 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: 0.010 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 303.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 47337 Z= 0.349 Angle : 0.753 12.405 64352 Z= 0.401 Chirality : 0.047 0.214 7196 Planarity : 0.005 0.075 7986 Dihedral : 15.476 177.917 18186 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.31 (0.11), residues: 5484 helix: -0.16 (0.12), residues: 1716 sheet: -1.22 (0.14), residues: 1113 loop : -1.10 (0.12), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1334 HIS 0.015 0.002 HIS C 66 PHE 0.044 0.002 PHE b 693 TYR 0.026 0.002 TYR K 81 ARG 0.019 0.001 ARG a 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 1027 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1027 time to evaluate : 5.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 CYS cc_start: 0.5980 (t) cc_final: 0.5678 (t) REVERT: A 535 MET cc_start: 0.8280 (ptp) cc_final: 0.8016 (ptp) REVERT: A 763 TYR cc_start: 0.8304 (m-80) cc_final: 0.7968 (m-80) REVERT: A 769 MET cc_start: 0.9547 (mtm) cc_final: 0.9308 (mtt) REVERT: A 1086 MET cc_start: 0.9016 (mmm) cc_final: 0.8789 (mmm) REVERT: A 1155 LYS cc_start: 0.7636 (tppp) cc_final: 0.7271 (ttpp) REVERT: A 1162 GLU cc_start: 0.7748 (tt0) cc_final: 0.7518 (tt0) REVERT: A 1381 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 1422 GLN cc_start: 0.8111 (pt0) cc_final: 0.7899 (pt0) REVERT: A 1459 MET cc_start: 0.8173 (mtp) cc_final: 0.7763 (mtp) REVERT: B 155 MET cc_start: 0.9162 (ttm) cc_final: 0.8794 (ttm) REVERT: B 298 MET cc_start: 0.7232 (mmt) cc_final: 0.6639 (mmt) REVERT: B 346 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7198 (mt-10) REVERT: B 386 ASP cc_start: 0.8000 (m-30) cc_final: 0.7782 (m-30) REVERT: B 1091 ARG cc_start: 0.8890 (ttp80) cc_final: 0.8659 (ttp80) REVERT: B 1163 MET cc_start: 0.8288 (mtp) cc_final: 0.8080 (mtm) REVERT: E 69 THR cc_start: 0.8334 (p) cc_final: 0.8123 (p) REVERT: E 125 TYR cc_start: 0.7044 (m-80) cc_final: 0.5979 (m-80) REVERT: E 137 ILE cc_start: 0.8676 (pt) cc_final: 0.8470 (pt) REVERT: E 151 MET cc_start: 0.8397 (mtp) cc_final: 0.8111 (mtp) REVERT: G 11 ILE cc_start: 0.6730 (tp) cc_final: 0.5970 (mt) REVERT: H 55 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7672 (ttpt) REVERT: H 92 MET cc_start: 0.8689 (mtm) cc_final: 0.8179 (mtm) REVERT: I 14 ILE cc_start: 0.8374 (tt) cc_final: 0.7791 (tp) REVERT: I 44 TYR cc_start: 0.8231 (t80) cc_final: 0.7584 (t80) REVERT: K 102 GLU cc_start: 0.7558 (tt0) cc_final: 0.7337 (tt0) REVERT: L 16 ILE cc_start: 0.7310 (pt) cc_final: 0.7004 (mp) REVERT: a 188 GLU cc_start: 0.7155 (pm20) cc_final: 0.6952 (pm20) outliers start: 0 outliers final: 2 residues processed: 1027 average time/residue: 3.2144 time to fit residues: 4034.2501 Evaluate side-chains 732 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 730 time to evaluate : 5.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain d residue 231 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 470 optimal weight: 1.9990 chunk 422 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 284 optimal weight: 30.0000 chunk 225 optimal weight: 20.0000 chunk 436 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 324 optimal weight: 20.0000 chunk 505 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 711 GLN A 926 ASN A1077 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN B1049 GLN ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN I 56 ASN I 98 GLN b 927 ASN ** d 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 908 ASN d1111 ASN a 180 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 47337 Z= 0.326 Angle : 0.605 10.790 64352 Z= 0.318 Chirality : 0.044 0.196 7196 Planarity : 0.005 0.060 7986 Dihedral : 13.489 177.209 7107 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.43 % Allowed : 10.12 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.11), residues: 5484 helix: 0.40 (0.13), residues: 1705 sheet: -0.91 (0.14), residues: 1122 loop : -0.90 (0.12), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 479 HIS 0.008 0.001 HIS B 144 PHE 0.026 0.002 PHE G 107 TYR 0.019 0.002 TYR I 37 ARG 0.007 0.001 ARG B1062 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 832 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 762 time to evaluate : 5.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7072 (mpt180) REVERT: A 112 PHE cc_start: 0.8553 (t80) cc_final: 0.8238 (t80) REVERT: A 535 MET cc_start: 0.8249 (ptp) cc_final: 0.7963 (ptp) REVERT: A 711 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7788 (tm130) REVERT: A 769 MET cc_start: 0.9538 (mtm) cc_final: 0.9232 (mtt) REVERT: A 1086 MET cc_start: 0.9085 (mmm) cc_final: 0.8799 (mmm) REVERT: A 1155 LYS cc_start: 0.7725 (tppp) cc_final: 0.7348 (ttpp) REVERT: A 1422 GLN cc_start: 0.8066 (pt0) cc_final: 0.7850 (pt0) REVERT: B 297 MET cc_start: 0.8433 (mtt) cc_final: 0.8192 (mtt) REVERT: B 298 MET cc_start: 0.7430 (mmt) cc_final: 0.6811 (mmt) REVERT: B 346 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7176 (mt-10) REVERT: B 611 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: B 914 GLU cc_start: 0.7122 (pp20) cc_final: 0.6861 (pp20) REVERT: B 1136 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: D 22 PHE cc_start: 0.6859 (m-10) cc_final: 0.6372 (m-80) REVERT: E 30 GLN cc_start: 0.7815 (tp40) cc_final: 0.7517 (tp-100) REVERT: G 97 LEU cc_start: 0.7000 (tt) cc_final: 0.6728 (tt) REVERT: H 92 MET cc_start: 0.8984 (mtm) cc_final: 0.8704 (mtm) REVERT: I 14 ILE cc_start: 0.8255 (tt) cc_final: 0.7814 (tt) REVERT: I 44 TYR cc_start: 0.8271 (t80) cc_final: 0.7839 (t80) REVERT: J 26 GLN cc_start: 0.7375 (mt0) cc_final: 0.7006 (mt0) REVERT: K 22 ASN cc_start: 0.8426 (m-40) cc_final: 0.8188 (m110) REVERT: K 102 GLU cc_start: 0.7631 (tt0) cc_final: 0.7412 (tt0) REVERT: d 1111 ASN cc_start: 0.6710 (m-40) cc_final: 0.6481 (m110) outliers start: 70 outliers final: 23 residues processed: 796 average time/residue: 3.2498 time to fit residues: 3165.0595 Evaluate side-chains 749 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 722 time to evaluate : 5.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain b residue 520 GLU Chi-restraints excluded: chain b residue 569 THR Chi-restraints excluded: chain b residue 1394 ARG Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain a residue 183 GLN Chi-restraints excluded: chain a residue 331 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 chunk 420 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 506 optimal weight: 3.9990 chunk 547 optimal weight: 2.9990 chunk 451 optimal weight: 1.9990 chunk 502 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 406 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN A 926 ASN A 935 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 314 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN b 706 GLN d 107 ASN d1049 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 47337 Z= 0.353 Angle : 0.601 10.632 64352 Z= 0.317 Chirality : 0.044 0.200 7196 Planarity : 0.005 0.057 7986 Dihedral : 13.425 177.252 7103 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.34 % Allowed : 12.44 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.67 (0.11), residues: 5484 helix: 0.51 (0.13), residues: 1701 sheet: -0.80 (0.15), residues: 1103 loop : -0.83 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1192 HIS 0.007 0.001 HIS B 144 PHE 0.028 0.002 PHE G 107 TYR 0.037 0.002 TYR B 916 ARG 0.011 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 820 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 754 time to evaluate : 5.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8473 (m-80) cc_final: 0.8254 (m-80) REVERT: A 112 PHE cc_start: 0.8588 (t80) cc_final: 0.8238 (t80) REVERT: A 239 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6658 (tp30) REVERT: A 535 MET cc_start: 0.8268 (ptp) cc_final: 0.7991 (ptp) REVERT: A 1155 LYS cc_start: 0.7684 (tppp) cc_final: 0.7316 (ttpp) REVERT: A 1350 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8294 (mtpm) REVERT: A 1422 GLN cc_start: 0.8100 (pt0) cc_final: 0.7814 (pt0) REVERT: B 296 GLU cc_start: 0.7278 (mp0) cc_final: 0.7015 (mp0) REVERT: B 297 MET cc_start: 0.8448 (mtt) cc_final: 0.8198 (mtt) REVERT: B 298 MET cc_start: 0.7560 (mmt) cc_final: 0.7025 (mmt) REVERT: B 611 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: B 764 MET cc_start: 0.9149 (mtt) cc_final: 0.8649 (mtp) REVERT: B 1136 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7302 (pp20) REVERT: C 86 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7358 (mtt180) REVERT: E 30 GLN cc_start: 0.7858 (tp40) cc_final: 0.7586 (tp-100) REVERT: H 92 MET cc_start: 0.8923 (mtm) cc_final: 0.8697 (mtm) REVERT: J 26 GLN cc_start: 0.7419 (mt0) cc_final: 0.7068 (mt0) REVERT: K 22 ASN cc_start: 0.8479 (m-40) cc_final: 0.8207 (m110) REVERT: L 16 ILE cc_start: 0.7691 (pt) cc_final: 0.7156 (mp) REVERT: b 761 GLU cc_start: 0.7149 (tp30) cc_final: 0.6771 (pp20) outliers start: 66 outliers final: 35 residues processed: 782 average time/residue: 3.2228 time to fit residues: 3089.7227 Evaluate side-chains 764 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 725 time to evaluate : 5.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain b residue 569 THR Chi-restraints excluded: chain b residue 873 VAL Chi-restraints excluded: chain b residue 929 VAL Chi-restraints excluded: chain b residue 1394 ARG Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain d residue 1054 MET Chi-restraints excluded: chain a residue 101 SER Chi-restraints excluded: chain a residue 183 GLN Chi-restraints excluded: chain a residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 500 optimal weight: 2.9990 chunk 380 optimal weight: 0.6980 chunk 262 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 241 optimal weight: 0.8980 chunk 340 optimal weight: 2.9990 chunk 508 optimal weight: 0.9980 chunk 538 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 481 optimal weight: 3.9990 chunk 145 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN K 2 ASN d1111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 47337 Z= 0.181 Angle : 0.532 10.115 64352 Z= 0.279 Chirality : 0.042 0.165 7196 Planarity : 0.004 0.062 7986 Dihedral : 13.201 178.230 7103 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.22 % Allowed : 13.56 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.39 (0.11), residues: 5484 helix: 0.88 (0.13), residues: 1693 sheet: -0.77 (0.15), residues: 1087 loop : -0.71 (0.12), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1192 HIS 0.005 0.001 HIS B 144 PHE 0.017 0.001 PHE d1030 TYR 0.036 0.001 TYR G 3 ARG 0.009 0.000 ARG b 994 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 814 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 754 time to evaluate : 5.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8466 (m-80) cc_final: 0.8152 (m-80) REVERT: A 112 PHE cc_start: 0.8534 (t80) cc_final: 0.8224 (t80) REVERT: A 535 MET cc_start: 0.8251 (ptp) cc_final: 0.7989 (ptp) REVERT: A 1155 LYS cc_start: 0.7669 (tppp) cc_final: 0.7293 (ttpp) REVERT: A 1350 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8316 (mtpm) REVERT: A 1422 GLN cc_start: 0.8064 (pt0) cc_final: 0.7806 (pt0) REVERT: B 297 MET cc_start: 0.8378 (mtt) cc_final: 0.8113 (mtt) REVERT: B 298 MET cc_start: 0.7473 (mmt) cc_final: 0.6960 (mmt) REVERT: B 764 MET cc_start: 0.9127 (mtt) cc_final: 0.8916 (mtt) REVERT: B 1136 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: E 30 GLN cc_start: 0.7842 (tp40) cc_final: 0.7586 (tp-100) REVERT: J 26 GLN cc_start: 0.7370 (mt0) cc_final: 0.7055 (mt0) REVERT: L 16 ILE cc_start: 0.7638 (pt) cc_final: 0.7091 (mp) REVERT: b 706 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6994 (mp10) outliers start: 60 outliers final: 32 residues processed: 780 average time/residue: 3.1946 time to fit residues: 3062.0875 Evaluate side-chains 761 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 727 time to evaluate : 5.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain b residue 569 THR Chi-restraints excluded: chain b residue 637 ARG Chi-restraints excluded: chain b residue 706 GLN Chi-restraints excluded: chain b residue 929 VAL Chi-restraints excluded: chain b residue 1394 ARG Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain d residue 969 GLU Chi-restraints excluded: chain a residue 183 GLN Chi-restraints excluded: chain a residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 448 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 400 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 459 optimal weight: 0.7980 chunk 372 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 274 optimal weight: 0.9990 chunk 483 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 ASN A1129 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN d 904 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 47337 Z= 0.341 Angle : 0.582 10.149 64352 Z= 0.307 Chirality : 0.043 0.188 7196 Planarity : 0.005 0.064 7986 Dihedral : 13.255 176.880 7103 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.59 % Allowed : 14.22 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.45 (0.11), residues: 5484 helix: 0.75 (0.13), residues: 1704 sheet: -0.72 (0.14), residues: 1105 loop : -0.72 (0.12), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 479 HIS 0.007 0.001 HIS b 579 PHE 0.028 0.002 PHE G 107 TYR 0.034 0.002 TYR B 916 ARG 0.007 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 838 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 760 time to evaluate : 5.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8506 (m-80) cc_final: 0.8174 (m-80) REVERT: A 112 PHE cc_start: 0.8546 (t80) cc_final: 0.8248 (t80) REVERT: A 239 GLU cc_start: 0.6963 (tp30) cc_final: 0.6632 (tp30) REVERT: A 535 MET cc_start: 0.8274 (ptp) cc_final: 0.8025 (ptp) REVERT: A 1155 LYS cc_start: 0.7718 (tppp) cc_final: 0.7332 (ttpp) REVERT: A 1350 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8290 (mtpm) REVERT: A 1422 GLN cc_start: 0.8113 (pt0) cc_final: 0.7851 (pt0) REVERT: B 297 MET cc_start: 0.8506 (mtt) cc_final: 0.8249 (mtt) REVERT: B 298 MET cc_start: 0.7518 (mmt) cc_final: 0.6960 (mmt) REVERT: B 611 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: C 86 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7462 (mtt180) REVERT: C 213 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7169 (mm-30) REVERT: I 42 CYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7543 (p) REVERT: J 26 GLN cc_start: 0.7420 (mt0) cc_final: 0.7131 (mt0) REVERT: K 22 ASN cc_start: 0.8452 (m-40) cc_final: 0.8216 (m110) REVERT: L 16 ILE cc_start: 0.7650 (pt) cc_final: 0.7174 (mp) REVERT: L 51 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7650 (mtm180) REVERT: b 706 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: b 761 GLU cc_start: 0.7135 (tp30) cc_final: 0.6734 (pp20) outliers start: 78 outliers final: 44 residues processed: 795 average time/residue: 3.2964 time to fit residues: 3207.7148 Evaluate side-chains 779 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 731 time to evaluate : 5.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 42 CYS Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain b residue 569 THR Chi-restraints excluded: chain b residue 637 ARG Chi-restraints excluded: chain b residue 706 GLN Chi-restraints excluded: chain b residue 929 VAL Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain d residue 945 ILE Chi-restraints excluded: chain d residue 969 GLU Chi-restraints excluded: chain d residue 1054 MET Chi-restraints excluded: chain d residue 1064 SER Chi-restraints excluded: chain a residue 183 GLN Chi-restraints excluded: chain a residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 181 optimal weight: 2.9990 chunk 484 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 538 optimal weight: 3.9990 chunk 447 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 282 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 ASN A1129 ASN B 314 GLN B 500 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 9 GLN a 187 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 47337 Z= 0.256 Angle : 0.555 9.957 64352 Z= 0.292 Chirality : 0.042 0.159 7196 Planarity : 0.004 0.069 7986 Dihedral : 13.186 177.350 7103 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.41 % Allowed : 14.93 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.36 (0.11), residues: 5484 helix: 0.85 (0.13), residues: 1699 sheet: -0.75 (0.15), residues: 1090 loop : -0.64 (0.12), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1192 HIS 0.005 0.001 HIS B1053 PHE 0.019 0.001 PHE b 689 TYR 0.031 0.001 TYR B 916 ARG 0.008 0.000 ARG b 994 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 809 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 740 time to evaluate : 5.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8515 (m-80) cc_final: 0.8192 (m-80) REVERT: A 112 PHE cc_start: 0.8543 (t80) cc_final: 0.8263 (t80) REVERT: A 239 GLU cc_start: 0.6969 (tp30) cc_final: 0.6640 (tp30) REVERT: A 535 MET cc_start: 0.8258 (ptp) cc_final: 0.7994 (ptp) REVERT: A 868 MET cc_start: 0.8699 (mtm) cc_final: 0.8484 (mtm) REVERT: A 1155 LYS cc_start: 0.7699 (tppp) cc_final: 0.7333 (ttpp) REVERT: A 1350 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8290 (mtpm) REVERT: A 1422 GLN cc_start: 0.8095 (pt0) cc_final: 0.7846 (pt0) REVERT: B 52 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: B 297 MET cc_start: 0.8493 (mtt) cc_final: 0.8235 (mtt) REVERT: B 298 MET cc_start: 0.7496 (mmt) cc_final: 0.6947 (mmt) REVERT: C 41 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: C 86 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7462 (mtt180) REVERT: C 213 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7150 (mm-30) REVERT: E 18 MET cc_start: 0.8539 (mmt) cc_final: 0.8261 (mmp) REVERT: J 26 GLN cc_start: 0.7366 (mt0) cc_final: 0.7103 (mt0) REVERT: L 16 ILE cc_start: 0.7623 (pt) cc_final: 0.7138 (mp) REVERT: L 51 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7644 (mtm180) REVERT: b 599 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6994 (tp30) REVERT: b 706 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6995 (mp10) outliers start: 69 outliers final: 44 residues processed: 773 average time/residue: 3.2582 time to fit residues: 3094.7414 Evaluate side-chains 765 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 716 time to evaluate : 5.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain b residue 569 THR Chi-restraints excluded: chain b residue 599 GLU Chi-restraints excluded: chain b residue 637 ARG Chi-restraints excluded: chain b residue 706 GLN Chi-restraints excluded: chain b residue 929 VAL Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain d residue 945 ILE Chi-restraints excluded: chain d residue 969 GLU Chi-restraints excluded: chain d residue 1054 MET Chi-restraints excluded: chain a residue 183 GLN Chi-restraints excluded: chain a residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 519 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 307 optimal weight: 0.9980 chunk 393 optimal weight: 4.9990 chunk 304 optimal weight: 0.1980 chunk 453 optimal weight: 0.6980 chunk 300 optimal weight: 0.7980 chunk 536 optimal weight: 2.9990 chunk 335 optimal weight: 7.9990 chunk 327 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 ASN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 47337 Z= 0.188 Angle : 0.529 9.415 64352 Z= 0.276 Chirality : 0.041 0.187 7196 Planarity : 0.004 0.075 7986 Dihedral : 13.034 177.943 7103 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.28 % Allowed : 15.54 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.18 (0.11), residues: 5484 helix: 1.06 (0.13), residues: 1692 sheet: -0.71 (0.15), residues: 1089 loop : -0.55 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1192 HIS 0.004 0.001 HIS I 100 PHE 0.033 0.001 PHE G 107 TYR 0.041 0.001 TYR B 916 ARG 0.009 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 805 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 742 time to evaluate : 5.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8515 (m-80) cc_final: 0.8214 (m-80) REVERT: A 112 PHE cc_start: 0.8520 (t80) cc_final: 0.8274 (t80) REVERT: A 239 GLU cc_start: 0.6912 (tp30) cc_final: 0.6557 (tp30) REVERT: A 535 MET cc_start: 0.8216 (ptp) cc_final: 0.7910 (ptp) REVERT: A 1155 LYS cc_start: 0.7693 (tppp) cc_final: 0.7327 (ttpp) REVERT: A 1350 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8285 (mtpm) REVERT: A 1422 GLN cc_start: 0.8080 (pt0) cc_final: 0.7813 (pt0) REVERT: B 52 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7298 (mt0) REVERT: B 296 GLU cc_start: 0.7345 (mp0) cc_final: 0.7105 (mp0) REVERT: B 297 MET cc_start: 0.8447 (mtt) cc_final: 0.8197 (mtt) REVERT: B 298 MET cc_start: 0.7472 (mmt) cc_final: 0.6962 (mmt) REVERT: C 41 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: C 86 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7618 (mtt180) REVERT: C 213 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7114 (mm-30) REVERT: E 18 MET cc_start: 0.8543 (mmt) cc_final: 0.8270 (mmp) REVERT: J 26 GLN cc_start: 0.7394 (mt0) cc_final: 0.7171 (mt0) REVERT: L 16 ILE cc_start: 0.7567 (pt) cc_final: 0.7052 (mp) REVERT: L 27 GLU cc_start: 0.6515 (tm-30) cc_final: 0.6202 (tm-30) REVERT: L 51 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7644 (mtm180) REVERT: d 938 MET cc_start: 0.6203 (pmm) cc_final: 0.5968 (pmm) outliers start: 63 outliers final: 41 residues processed: 768 average time/residue: 3.2438 time to fit residues: 3046.5687 Evaluate side-chains 766 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 722 time to evaluate : 5.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain b residue 569 THR Chi-restraints excluded: chain b residue 637 ARG Chi-restraints excluded: chain b residue 929 VAL Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain d residue 945 ILE Chi-restraints excluded: chain d residue 969 GLU Chi-restraints excluded: chain d residue 1064 SER Chi-restraints excluded: chain a residue 183 GLN Chi-restraints excluded: chain a residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 332 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 320 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 341 optimal weight: 0.6980 chunk 365 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 421 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN b 706 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 47337 Z= 0.263 Angle : 0.554 9.703 64352 Z= 0.290 Chirality : 0.042 0.181 7196 Planarity : 0.004 0.080 7986 Dihedral : 13.043 177.439 7103 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.22 % Allowed : 15.85 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.21 (0.11), residues: 5484 helix: 1.01 (0.13), residues: 1699 sheet: -0.69 (0.15), residues: 1090 loop : -0.56 (0.12), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1192 HIS 0.005 0.001 HIS A 620 PHE 0.019 0.002 PHE b 689 TYR 0.037 0.001 TYR B 916 ARG 0.015 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 785 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 725 time to evaluate : 6.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8540 (m-80) cc_final: 0.8234 (m-80) REVERT: A 112 PHE cc_start: 0.8526 (t80) cc_final: 0.8281 (t80) REVERT: A 239 GLU cc_start: 0.6916 (tp30) cc_final: 0.6572 (tp30) REVERT: A 535 MET cc_start: 0.8252 (ptp) cc_final: 0.8001 (ptp) REVERT: A 868 MET cc_start: 0.8686 (mtm) cc_final: 0.8457 (mtm) REVERT: A 1155 LYS cc_start: 0.7726 (tppp) cc_final: 0.7344 (ttpp) REVERT: A 1350 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8301 (mtpm) REVERT: A 1422 GLN cc_start: 0.8084 (pt0) cc_final: 0.7860 (pt0) REVERT: B 52 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7318 (mt0) REVERT: B 297 MET cc_start: 0.8482 (mtt) cc_final: 0.8243 (mtt) REVERT: B 298 MET cc_start: 0.7490 (mmt) cc_final: 0.7031 (mmt) REVERT: B 358 GLU cc_start: 0.6929 (mp0) cc_final: 0.6643 (mp0) REVERT: C 41 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: C 86 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7587 (mtt180) REVERT: C 166 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8098 (mttt) REVERT: C 213 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7130 (mm-30) REVERT: G 11 ILE cc_start: 0.7093 (tp) cc_final: 0.6832 (tp) REVERT: I 40 ARG cc_start: 0.7253 (ptp-110) cc_final: 0.7040 (ptp-170) REVERT: J 26 GLN cc_start: 0.7394 (mt0) cc_final: 0.7153 (mt0) REVERT: L 16 ILE cc_start: 0.7597 (pt) cc_final: 0.7079 (mp) REVERT: L 51 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7638 (mtm180) outliers start: 60 outliers final: 46 residues processed: 754 average time/residue: 3.2605 time to fit residues: 3036.5805 Evaluate side-chains 764 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 714 time to evaluate : 5.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 893 GLU Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain b residue 569 THR Chi-restraints excluded: chain b residue 637 ARG Chi-restraints excluded: chain b residue 929 VAL Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain d residue 945 ILE Chi-restraints excluded: chain d residue 969 GLU Chi-restraints excluded: chain d residue 1064 SER Chi-restraints excluded: chain a residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 488 optimal weight: 2.9990 chunk 514 optimal weight: 4.9990 chunk 469 optimal weight: 0.4980 chunk 500 optimal weight: 2.9990 chunk 301 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 392 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 chunk 452 optimal weight: 0.9980 chunk 473 optimal weight: 2.9990 chunk 498 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 47337 Z= 0.238 Angle : 0.546 9.445 64352 Z= 0.285 Chirality : 0.042 0.199 7196 Planarity : 0.004 0.091 7986 Dihedral : 13.020 177.273 7103 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.28 % Allowed : 15.99 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.17 (0.11), residues: 5484 helix: 1.04 (0.13), residues: 1701 sheet: -0.67 (0.15), residues: 1092 loop : -0.54 (0.12), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1192 HIS 0.004 0.001 HIS A 620 PHE 0.040 0.001 PHE G 107 TYR 0.030 0.001 TYR B 916 ARG 0.012 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 800 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 737 time to evaluate : 5.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8526 (m-80) cc_final: 0.8239 (m-80) REVERT: A 112 PHE cc_start: 0.8525 (t80) cc_final: 0.8286 (t80) REVERT: A 239 GLU cc_start: 0.6918 (tp30) cc_final: 0.6578 (tp30) REVERT: A 535 MET cc_start: 0.8248 (ptp) cc_final: 0.7993 (ptp) REVERT: A 868 MET cc_start: 0.8701 (mtm) cc_final: 0.8485 (mtm) REVERT: A 1155 LYS cc_start: 0.7695 (tppp) cc_final: 0.7289 (ttpp) REVERT: A 1350 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8294 (mtpm) REVERT: A 1422 GLN cc_start: 0.8088 (pt0) cc_final: 0.7840 (pt0) REVERT: B 52 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7303 (mt0) REVERT: B 296 GLU cc_start: 0.7372 (mp0) cc_final: 0.7113 (mp0) REVERT: B 297 MET cc_start: 0.8491 (mtt) cc_final: 0.8253 (mtt) REVERT: B 298 MET cc_start: 0.7470 (mmt) cc_final: 0.7049 (mmt) REVERT: B 358 GLU cc_start: 0.6946 (mp0) cc_final: 0.6646 (mp0) REVERT: B 611 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6995 (mt-10) REVERT: C 41 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: C 86 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7546 (mtt180) REVERT: C 166 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8121 (mttt) REVERT: C 213 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7164 (mm-30) REVERT: G 11 ILE cc_start: 0.7180 (tp) cc_final: 0.6914 (tp) REVERT: I 40 ARG cc_start: 0.7247 (ptp-110) cc_final: 0.6922 (ptp-170) REVERT: J 26 GLN cc_start: 0.7460 (mt0) cc_final: 0.7250 (mt0) REVERT: L 51 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7627 (mtm180) outliers start: 63 outliers final: 46 residues processed: 766 average time/residue: 3.3012 time to fit residues: 3145.2675 Evaluate side-chains 782 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 731 time to evaluate : 5.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain b residue 569 THR Chi-restraints excluded: chain b residue 637 ARG Chi-restraints excluded: chain b residue 929 VAL Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain d residue 945 ILE Chi-restraints excluded: chain d residue 969 GLU Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain a residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 328 optimal weight: 2.9990 chunk 529 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 367 optimal weight: 0.8980 chunk 554 optimal weight: 1.9990 chunk 510 optimal weight: 0.8980 chunk 441 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN b 706 GLN d1111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 47337 Z= 0.308 Angle : 0.578 9.807 64352 Z= 0.303 Chirality : 0.043 0.212 7196 Planarity : 0.005 0.084 7986 Dihedral : 13.064 176.884 7103 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.10 % Allowed : 16.37 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.24 (0.11), residues: 5484 helix: 0.95 (0.13), residues: 1702 sheet: -0.68 (0.15), residues: 1096 loop : -0.58 (0.12), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1192 HIS 0.006 0.001 HIS b 579 PHE 0.021 0.002 PHE b 689 TYR 0.037 0.002 TYR B 916 ARG 0.020 0.001 ARG L 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1279 is missing expected H atoms. Skipping. Residue LYS 244 is missing expected H atoms. Skipping. Residue THR 827 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Evaluate side-chains 787 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 733 time to evaluate : 5.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8523 (m-80) cc_final: 0.8237 (m-80) REVERT: A 535 MET cc_start: 0.8283 (ptp) cc_final: 0.8017 (ptp) REVERT: A 868 MET cc_start: 0.8726 (mtm) cc_final: 0.8524 (mtm) REVERT: A 1155 LYS cc_start: 0.7686 (tppp) cc_final: 0.7292 (ttpp) REVERT: A 1350 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8315 (mtpm) REVERT: A 1422 GLN cc_start: 0.8076 (pt0) cc_final: 0.7837 (pt0) REVERT: B 52 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7313 (mt0) REVERT: B 296 GLU cc_start: 0.7392 (mp0) cc_final: 0.7145 (mp0) REVERT: B 297 MET cc_start: 0.8563 (mtt) cc_final: 0.8319 (mtt) REVERT: B 298 MET cc_start: 0.7467 (mmt) cc_final: 0.7048 (mmt) REVERT: B 358 GLU cc_start: 0.6868 (mp0) cc_final: 0.6613 (mp0) REVERT: C 41 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: C 86 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7554 (mtt180) REVERT: C 213 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7095 (mm-30) REVERT: E 18 MET cc_start: 0.8476 (mmt) cc_final: 0.8237 (mmp) REVERT: G 11 ILE cc_start: 0.7223 (tp) cc_final: 0.6957 (tp) REVERT: J 26 GLN cc_start: 0.7481 (mt0) cc_final: 0.7264 (mt0) REVERT: b 829 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6341 (tm-30) REVERT: d 1111 ASN cc_start: 0.6894 (m-40) cc_final: 0.6631 (m110) outliers start: 54 outliers final: 48 residues processed: 756 average time/residue: 3.2560 time to fit residues: 3042.2420 Evaluate side-chains 774 residues out of total 4911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 722 time to evaluate : 5.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 1135 LYS Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain b residue 569 THR Chi-restraints excluded: chain b residue 637 ARG Chi-restraints excluded: chain b residue 829 GLU Chi-restraints excluded: chain b residue 929 VAL Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain d residue 945 ILE Chi-restraints excluded: chain d residue 969 GLU Chi-restraints excluded: chain d residue 1064 SER Chi-restraints excluded: chain a residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 350 optimal weight: 0.6980 chunk 470 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 407 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 442 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 454 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118091 restraints weight = 137096.300| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.61 r_work: 0.2931 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 47337 Z= 0.193 Angle : 0.535 9.870 64352 Z= 0.279 Chirality : 0.042 0.201 7196 Planarity : 0.004 0.086 7986 Dihedral : 12.955 177.730 7103 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.98 % Allowed : 16.56 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.08 (0.11), residues: 5484 helix: 1.14 (0.13), residues: 1694 sheet: -0.64 (0.15), residues: 1084 loop : -0.49 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1192 HIS 0.004 0.001 HIS a 229 PHE 0.036 0.001 PHE G 107 TYR 0.030 0.001 TYR B 916 ARG 0.013 0.000 ARG E 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40612.70 seconds wall clock time: 696 minutes 20.04 seconds (41780.04 seconds total)