Starting phenix.real_space_refine on Sun Mar 17 01:00:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwr_14192/03_2024/7qwr_14192_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwr_14192/03_2024/7qwr_14192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwr_14192/03_2024/7qwr_14192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwr_14192/03_2024/7qwr_14192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwr_14192/03_2024/7qwr_14192_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qwr_14192/03_2024/7qwr_14192_neut.pdb" } resolution = 2.9 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3766 5.49 5 Mg 97 5.21 5 S 238 5.16 5 C 69919 2.51 5 N 25306 2.21 5 O 35245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "t TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 30": "OD1" <-> "OD2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 134576 Number of models: 1 Model: "" Number of chains: 55 Chain: "s" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "t" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 531 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "u" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1868 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3148 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "c" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2386 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "e" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "G" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1934 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "i" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "I" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1655 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1703 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "l" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "m" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "N" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "n" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 222 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "O" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "o" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "P" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "Q" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1506 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "r" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "S" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1454 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "T" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "U" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 859 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain: "V" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "5" Number of atoms: 74854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3493, 74854 Classifications: {'RNA': 3493} Modifications used: {'5*END': 1, 'rna2p_pur': 329, 'rna2p_pyr': 219, 'rna3p_pur': 1575, 'rna3p_pyr': 1369} Link IDs: {'rna2p': 548, 'rna3p': 2944} Chain breaks: 15 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 976 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "7" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "8" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 67} Link IDs: {'rna2p': 26, 'rna3p': 129} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Unusual residues: {' MG': 96} Classifications: {'undetermined': 96} Link IDs: {None: 95} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20065 SG CYS g 46 61.806 72.357 112.202 1.00 26.78 S ATOM 20082 SG CYS g 49 60.986 70.699 115.608 1.00 24.14 S ATOM 20345 SG CYS g 83 60.895 68.564 112.495 1.00 25.00 S ATOM 20365 SG CYS g 86 58.321 71.276 112.914 1.00 32.89 S ATOM 27693 SG CYS j 19 110.733 92.848 87.315 1.00 11.51 S ATOM 27721 SG CYS j 22 114.155 94.499 87.452 1.00 11.35 S ATOM 27812 SG CYS j 34 111.299 95.920 89.490 1.00 9.11 S ATOM 27831 SG CYS j 37 111.335 96.405 85.763 1.00 9.03 S ATOM 33626 SG CYS m 96 159.171 146.341 179.358 1.00 14.35 S ATOM 33652 SG CYS m 99 160.132 142.716 178.759 1.00 16.91 S ATOM 33742 SG CYS m 110 162.739 145.044 180.168 1.00 12.94 S ATOM 33786 SG CYS m 115 161.688 145.398 176.563 1.00 15.24 S ATOM 37545 SG CYS o 12 104.448 188.633 90.487 1.00 17.44 S ATOM 37569 SG CYS o 15 103.176 191.656 88.568 1.00 22.32 S ATOM 38038 SG CYS o 72 100.935 189.923 91.359 1.00 19.89 S ATOM 38075 SG CYS o 77 101.530 188.301 87.970 1.00 37.40 S ATOM 39847 SG CYS p 39 56.424 81.325 126.209 1.00 13.79 S ATOM 39870 SG CYS p 42 56.153 77.860 127.560 1.00 16.46 S ATOM 39992 SG CYS p 57 59.561 79.230 126.125 1.00 11.60 S ATOM 40008 SG CYS p 60 56.569 78.093 123.932 1.00 14.54 S Time building chain proxies: 49.56, per 1000 atoms: 0.37 Number of scatterers: 134576 At special positions: 0 Unit cell: (260.28, 261.36, 224.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 238 16.00 P 3766 15.00 Mg 97 11.99 O 35245 8.00 N 25306 7.00 C 69919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 51.44 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 115 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 99 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 110 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 96 " pdb=" ZN o 201 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 72 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " Number of angles added : 30 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12394 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 72 sheets defined 37.0% alpha, 15.2% beta 1169 base pairs and 1781 stacking pairs defined. Time for finding SS restraints: 44.44 Creating SS restraints... Processing helix chain 't' and resid 70 through 83 removed outlier: 3.741A pdb=" N LEU t 83 " --> pdb=" O ALA t 79 " (cutoff:3.500A) Processing helix chain 'u' and resid 7 through 19 removed outlier: 3.891A pdb=" N ARG u 19 " --> pdb=" O GLN u 15 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 50 Processing helix chain 'u' and resid 102 through 107 removed outlier: 3.599A pdb=" N LEU u 107 " --> pdb=" O LEU u 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.749A pdb=" N ARG A 17 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.514A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.705A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'b' and resid 11 through 19 removed outlier: 3.530A pdb=" N LYS b 15 " --> pdb=" O ASN b 11 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 49 Processing helix chain 'b' and resid 50 through 52 No H-bonds generated for 'chain 'b' and resid 50 through 52' Processing helix chain 'b' and resid 53 through 76 Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.578A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 117 removed outlier: 3.775A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 139 through 157 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.922A pdb=" N ASN B 302 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'c' and resid 14 through 25 Processing helix chain 'c' and resid 30 through 41 Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 85 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.701A pdb=" N VAL C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.671A pdb=" N VAL C 158 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 removed outlier: 3.502A pdb=" N ALA C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.656A pdb=" N LYS C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 288 through 294 removed outlier: 3.512A pdb=" N ILE C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 321 through 329 removed outlier: 3.699A pdb=" N MET C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 338 Processing helix chain 'C' and resid 340 through 363 Processing helix chain 'd' and resid 37 through 39 No H-bonds generated for 'chain 'd' and resid 37 through 39' Processing helix chain 'd' and resid 40 through 57 removed outlier: 3.674A pdb=" N LEU d 46 " --> pdb=" O ALA d 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'D' and resid 9 through 15 removed outlier: 3.551A pdb=" N PHE D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 29 through 37 removed outlier: 4.003A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 removed outlier: 3.788A pdb=" N TYR D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 113 Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.563A pdb=" N GLY D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.858A pdb=" N ALA D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 Processing helix chain 'D' and resid 227 through 231 removed outlier: 3.577A pdb=" N ASN D 230 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D 231 " --> pdb=" O LYS D 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 231' Processing helix chain 'D' and resid 235 through 250 removed outlier: 4.132A pdb=" N LYS D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 292 Processing helix chain 'e' and resid 57 through 61 Processing helix chain 'e' and resid 81 through 87 removed outlier: 3.719A pdb=" N VAL e 87 " --> pdb=" O LYS e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 90 No H-bonds generated for 'chain 'e' and resid 88 through 90' Processing helix chain 'e' and resid 104 through 118 removed outlier: 3.833A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 62 Processing helix chain 'E' and resid 128 through 132 removed outlier: 3.532A pdb=" N HIS E 132 " --> pdb=" O PHE E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 209 through 213 Processing helix chain 'E' and resid 239 through 259 removed outlier: 3.999A pdb=" N LYS E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 263 through 269 Processing helix chain 'f' and resid 38 through 43 removed outlier: 3.769A pdb=" N PHE f 41 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU f 43 " --> pdb=" O GLU f 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 80 removed outlier: 3.674A pdb=" N ILE F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA F 80 " --> pdb=" O MET F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 114 Processing helix chain 'F' and resid 128 through 138 removed outlier: 3.603A pdb=" N VAL F 138 " --> pdb=" O MET F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 159 removed outlier: 3.643A pdb=" N VAL F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 182 removed outlier: 4.245A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 198 Processing helix chain 'F' and resid 202 through 210 removed outlier: 3.635A pdb=" N LEU F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 Processing helix chain 'g' and resid 61 through 66 Processing helix chain 'g' and resid 69 through 73 removed outlier: 3.771A pdb=" N HIS g 73 " --> pdb=" O THR g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 115 Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.686A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 Processing helix chain 'G' and resid 88 through 100 removed outlier: 3.745A pdb=" N GLN G 94 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 103 No H-bonds generated for 'chain 'G' and resid 101 through 103' Processing helix chain 'G' and resid 109 through 120 removed outlier: 3.851A pdb=" N ARG G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 169 through 178 Processing helix chain 'G' and resid 186 through 194 removed outlier: 3.868A pdb=" N LEU G 190 " --> pdb=" O GLY G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 221 Processing helix chain 'G' and resid 229 through 235 Processing helix chain 'G' and resid 243 through 260 Processing helix chain 'h' and resid 5 through 12 removed outlier: 4.172A pdb=" N GLY h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 37 Processing helix chain 'h' and resid 40 through 73 removed outlier: 3.839A pdb=" N ILE h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 88 through 93 Processing helix chain 'h' and resid 104 through 114 removed outlier: 3.540A pdb=" N TYR h 114 " --> pdb=" O LYS h 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 52 Processing helix chain 'H' and resid 63 through 86 removed outlier: 4.175A pdb=" N ALA H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.575A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 30 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 63 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 102 Processing helix chain 'I' and resid 5 through 10 removed outlier: 4.032A pdb=" N ARG I 10 " --> pdb=" O ARG I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 80 Processing helix chain 'I' and resid 144 through 157 removed outlier: 3.729A pdb=" N VAL I 149 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 187 removed outlier: 4.319A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU I 187 " --> pdb=" O ASP I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 212 removed outlier: 4.050A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'j' and resid 6 through 11 removed outlier: 3.667A pdb=" N GLY j 9 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG j 11 " --> pdb=" O PHE j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 57 removed outlier: 3.701A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 75 removed outlier: 3.917A pdb=" N ARG j 75 " --> pdb=" O TYR j 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 45 removed outlier: 3.945A pdb=" N ALA J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.717A pdb=" N PHE J 99 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 143 removed outlier: 3.901A pdb=" N ILE J 141 " --> pdb=" O GLY J 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA J 142 " --> pdb=" O PHE J 139 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP J 143 " --> pdb=" O SER J 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 138 through 143' Processing helix chain 'J' and resid 158 through 170 removed outlier: 3.595A pdb=" N TYR J 170 " --> pdb=" O PHE J 166 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 16 removed outlier: 3.524A pdb=" N PHE k 11 " --> pdb=" O GLU k 7 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 58 removed outlier: 4.071A pdb=" N GLN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 90 through 95 Processing helix chain 'L' and resid 107 through 123 Processing helix chain 'L' and resid 139 through 143 Processing helix chain 'L' and resid 170 through 175 removed outlier: 3.683A pdb=" N LYS L 174 " --> pdb=" O THR L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 211 removed outlier: 5.616A pdb=" N GLY L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE L 194 " --> pdb=" O ARG L 190 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 20 Processing helix chain 'l' and resid 24 through 30 removed outlier: 3.506A pdb=" N ILE l 27 " --> pdb=" O PRO l 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 81 Processing helix chain 'M' and resid 81 through 89 Processing helix chain 'M' and resid 89 through 103 Processing helix chain 'M' and resid 105 through 139 removed outlier: 3.864A pdb=" N MET M 118 " --> pdb=" O LYS M 114 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 91 removed outlier: 3.777A pdb=" N ALA m 86 " --> pdb=" O LEU m 82 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS m 88 " --> pdb=" O GLN m 84 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.739A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 removed outlier: 3.719A pdb=" N ARG N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 165 through 171 removed outlier: 3.830A pdb=" N SER N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 196 Processing helix chain 'n' and resid 3 through 24 removed outlier: 3.586A pdb=" N SER n 24 " --> pdb=" O MET n 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 29 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 59 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 109 through 114 removed outlier: 4.383A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 185 Processing helix chain 'O' and resid 185 through 195 removed outlier: 5.271A pdb=" N ARG O 191 " --> pdb=" O LYS O 187 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N PHE O 192 " --> pdb=" O LYS O 188 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL O 195 " --> pdb=" O ARG O 191 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 45 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 54 through 66 Processing helix chain 'P' and resid 69 through 82 Processing helix chain 'P' and resid 100 through 106 Processing helix chain 'P' and resid 113 through 135 removed outlier: 3.611A pdb=" N ALA P 117 " --> pdb=" O PRO P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'p' and resid 8 through 15 removed outlier: 3.888A pdb=" N VAL p 11 " --> pdb=" O VAL p 8 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY p 15 " --> pdb=" O GLY p 12 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 34 removed outlier: 4.008A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 53 removed outlier: 4.161A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 106 through 117 removed outlier: 3.582A pdb=" N GLY Q 117 " --> pdb=" O ILE Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 142 through 151 removed outlier: 4.358A pdb=" N ARG Q 146 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU Q 147 " --> pdb=" O LYS Q 144 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL Q 148 " --> pdb=" O GLY Q 145 " (cutoff:3.500A) Processing helix chain 'r' and resid 3 through 11 Processing helix chain 'r' and resid 87 through 98 removed outlier: 3.517A pdb=" N SER r 91 " --> pdb=" O ARG r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 103 through 105 No H-bonds generated for 'chain 'r' and resid 103 through 105' Processing helix chain 'r' and resid 106 through 121 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 33 Processing helix chain 'R' and resid 40 through 47 Processing helix chain 'R' and resid 60 through 73 removed outlier: 3.575A pdb=" N LYS R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 Processing helix chain 'R' and resid 116 through 128 Processing helix chain 'R' and resid 134 through 181 removed outlier: 3.551A pdb=" N LEU R 138 " --> pdb=" O ASN R 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 101 through 118 Processing helix chain 'S' and resid 120 through 122 No H-bonds generated for 'chain 'S' and resid 120 through 122' Processing helix chain 'S' and resid 139 through 144 Processing helix chain 'T' and resid 100 through 118 removed outlier: 3.703A pdb=" N PHE T 105 " --> pdb=" O SER T 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 32 removed outlier: 3.776A pdb=" N GLY U 32 " --> pdb=" O PRO U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 47 Processing helix chain 'U' and resid 53 through 58 removed outlier: 3.943A pdb=" N LEU U 56 " --> pdb=" O ALA U 53 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY U 57 " --> pdb=" O GLY U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 95 removed outlier: 3.689A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 73 Processing helix chain 'V' and resid 122 through 129 Processing helix chain 'V' and resid 129 through 136 removed outlier: 3.728A pdb=" N ASN V 135 " --> pdb=" O ARG V 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 42 Processing helix chain 'W' and resid 52 through 59 removed outlier: 3.552A pdb=" N ARG W 56 " --> pdb=" O THR W 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 76 Processing helix chain 'X' and resid 83 through 92 removed outlier: 3.774A pdb=" N LYS X 89 " --> pdb=" O SER X 85 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE X 90 " --> pdb=" O ALA X 86 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU X 91 " --> pdb=" O MET X 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 118 removed outlier: 3.545A pdb=" N LYS X 115 " --> pdb=" O GLN X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 152 removed outlier: 3.712A pdb=" N LYS X 152 " --> pdb=" O ASP X 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 20 removed outlier: 3.532A pdb=" N ASN Y 14 " --> pdb=" O ASP Y 10 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG Y 15 " --> pdb=" O ARG Y 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG Y 17 " --> pdb=" O LYS Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 30 removed outlier: 4.068A pdb=" N LYS Y 28 " --> pdb=" O HIS Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 134 removed outlier: 3.700A pdb=" N LYS Y 117 " --> pdb=" O LYS Y 113 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE Y 118 " --> pdb=" O ASP Y 114 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER Y 125 " --> pdb=" O ARG Y 121 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG Y 126 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY Y 133 " --> pdb=" O GLY Y 129 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 66 removed outlier: 3.535A pdb=" N ALA Z 63 " --> pdb=" O LYS Z 59 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 123 removed outlier: 3.572A pdb=" N LYS Z 109 " --> pdb=" O ALA Z 105 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG Z 112 " --> pdb=" O ARG Z 108 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE Z 118 " --> pdb=" O ALA Z 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 6 Processing helix chain 'a' and resid 7 through 12 removed outlier: 3.995A pdb=" N ARG a 12 " --> pdb=" O ARG a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 76 through 82 removed outlier: 5.478A pdb=" N TRP a 79 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR a 80 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU a 81 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL a 82 " --> pdb=" O TRP a 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 76 through 82' Processing helix chain 'a' and resid 83 through 89 removed outlier: 3.799A pdb=" N ARG a 87 " --> pdb=" O SER a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 107 Processing helix chain 'a' and resid 130 through 141 Processing sheet with id=AA1, first strand: chain 't' and resid 86 through 88 removed outlier: 4.586A pdb=" N VAL t 111 " --> pdb=" O VAL t 88 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL u 79 " --> pdb=" O ILE u 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 't' and resid 127 through 130 removed outlier: 3.553A pdb=" N ILE t 102 " --> pdb=" O LYS t 98 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG t 93 " --> pdb=" O PHE u 65 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR t 95 " --> pdb=" O ASN u 63 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU u 61 " --> pdb=" O ARG t 97 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR u 70 " --> pdb=" O THR u 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'u' and resid 30 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 77 removed outlier: 4.006A pdb=" N ASP A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 62 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL A 45 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ARG A 64 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLY A 43 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.817A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N HIS A 139 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS A 145 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA7, first strand: chain 'B' and resid 365 through 368 removed outlier: 7.454A pdb=" N LEU B 365 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU B 59 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE B 330 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE B 287 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET B 332 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LYS B 283 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N THR B 278 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLY B 221 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE B 280 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 219 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.255A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR B 104 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL B 87 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL B 86 " --> pdb=" O HIS B 165 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N HIS B 165 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 88 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 159 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.255A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR B 104 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL B 87 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 225 through 229 Processing sheet with id=AB2, first strand: chain 'B' and resid 292 through 293 removed outlier: 4.319A pdb=" N LEU B 292 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 298 " --> pdb=" O LEU B 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'c' and resid 26 through 29 removed outlier: 3.618A pdb=" N ASP c 98 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL c 28 " --> pdb=" O ILE c 96 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE c 96 " --> pdb=" O VAL c 28 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL c 46 " --> pdb=" O HIS c 72 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR c 74 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU c 48 " --> pdb=" O TYR c 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 7 through 9 Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AB6, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.276A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 253 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 230 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB8, first strand: chain 'd' and resid 21 through 28 removed outlier: 3.750A pdb=" N VAL d 21 " --> pdb=" O ARG d 90 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG d 63 " --> pdb=" O VAL d 106 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR d 108 " --> pdb=" O ARG d 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 72 through 79 removed outlier: 7.062A pdb=" N ILE D 64 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA D 77 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS D 62 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR D 79 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE D 60 " --> pdb=" O TYR D 79 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 59 " --> pdb=" O THR D 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 142 through 143 removed outlier: 5.991A pdb=" N PHE D 142 " --> pdb=" O SER D 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 183 through 184 removed outlier: 3.695A pdb=" N GLU D 189 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 75 through 79 Processing sheet with id=AC4, first strand: chain 'E' and resid 183 through 185 removed outlier: 4.092A pdb=" N LYS E 162 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR E 144 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N THR E 195 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE E 147 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR E 193 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 7 through 16 removed outlier: 5.722A pdb=" N PHE f 11 " --> pdb=" O LYS f 29 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS f 29 " --> pdb=" O PHE f 11 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY f 13 " --> pdb=" O LEU f 27 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR f 25 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N HIS f 24 " --> pdb=" O PHE f 88 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE f 88 " --> pdb=" O HIS f 24 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET f 83 " --> pdb=" O ALA f 77 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA f 77 " --> pdb=" O MET f 83 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG f 85 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS f 66 " --> pdb=" O ALA f 53 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL f 50 " --> pdb=" O ARG f 100 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG f 100 " --> pdb=" O VAL f 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 82 through 84 Processing sheet with id=AC7, first strand: chain 'F' and resid 213 through 214 removed outlier: 4.207A pdb=" N ASN F 121 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 161 through 164 Processing sheet with id=AC9, first strand: chain 'g' and resid 20 through 24 removed outlier: 3.549A pdb=" N VAL g 31 " --> pdb=" O SER g 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 181 through 184 removed outlier: 6.480A pdb=" N VAL G 155 " --> pdb=" O CYS G 182 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE G 157 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU G 154 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'h' and resid 119 through 120 Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 11 removed outlier: 7.161A pdb=" N ILE H 4 " --> pdb=" O TRP H 61 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 17 through 21 removed outlier: 3.698A pdb=" N THR H 24 " --> pdb=" O LYS H 21 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 133 through 136 removed outlier: 6.889A pdb=" N ARG H 89 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS H 184 " --> pdb=" O ARG H 89 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS H 91 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 102 through 105 Processing sheet with id=AD7, first strand: chain 'I' and resid 35 through 37 removed outlier: 6.907A pdb=" N MET I 52 " --> pdb=" O ILE I 135 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER I 137 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY I 50 " --> pdb=" O SER I 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 58 through 61 removed outlier: 5.666A pdb=" N ILE I 99 " --> pdb=" O PRO I 122 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY I 124 " --> pdb=" O ILE I 97 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 190 through 193 Processing sheet with id=AE1, first strand: chain 'j' and resid 16 through 18 Processing sheet with id=AE2, first strand: chain 'J' and resid 49 through 51 removed outlier: 3.618A pdb=" N ALA J 69 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL J 133 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU J 20 " --> pdb=" O TYR J 131 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR J 131 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU J 22 " --> pdb=" O ASP J 129 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP J 129 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'k' and resid 3 through 5 removed outlier: 4.238A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 22 through 24 Processing sheet with id=AE5, first strand: chain 'L' and resid 58 through 60 Processing sheet with id=AE6, first strand: chain 'M' and resid 7 through 8 removed outlier: 3.600A pdb=" N PHE S 152 " --> pdb=" O VAL M 7 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 45 through 50 removed outlier: 4.815A pdb=" N ARG M 46 " --> pdb=" O GLY M 40 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY M 40 " --> pdb=" O ARG M 46 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ARG M 35 " --> pdb=" O VAL M 30 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL M 30 " --> pdb=" O ARG M 35 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU M 37 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE M 60 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR M 14 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR M 58 " --> pdb=" O TYR M 14 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'm' and resid 102 through 103 Processing sheet with id=AE9, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.378A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY N 122 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU N 116 " --> pdb=" O ILE N 135 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 6 through 10 removed outlier: 6.103A pdb=" N LEU O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL O 36 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AF3, first strand: chain 'o' and resid 7 through 11 Processing sheet with id=AF4, first strand: chain 'P' and resid 14 through 51 removed outlier: 4.257A pdb=" N ASN P 50 " --> pdb=" O CYS P 173 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS P 173 " --> pdb=" O ASN P 50 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR P 180 " --> pdb=" O ILE P 143 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE P 143 " --> pdb=" O THR P 180 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 155 through 160 removed outlier: 3.899A pdb=" N ARG P 164 " --> pdb=" O ARG P 160 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'p' and resid 37 through 38 removed outlier: 6.776A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.558A pdb=" N LEU Q 61 " --> pdb=" O THR Q 87 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 119 through 121 removed outlier: 6.444A pdb=" N THR Q 79 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'r' and resid 17 through 18 Processing sheet with id=AG1, first strand: chain 'r' and resid 49 through 53 Processing sheet with id=AG2, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AG3, first strand: chain 'S' and resid 59 through 66 removed outlier: 5.581A pdb=" N ILE S 61 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG S 15 " --> pdb=" O ILE S 61 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 91 through 99 removed outlier: 3.727A pdb=" N ASN S 77 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS S 128 " --> pdb=" O TRP S 81 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG S 83 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE S 126 " --> pdb=" O ARG S 83 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 83 through 92 removed outlier: 6.483A pdb=" N VAL T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL T 64 " --> pdb=" O VAL T 75 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLY T 62 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 19 through 24 Processing sheet with id=AG7, first strand: chain 'U' and resid 100 through 103 Processing sheet with id=AG8, first strand: chain 'V' and resid 20 through 21 Processing sheet with id=AG9, first strand: chain 'V' and resid 25 through 28 removed outlier: 6.792A pdb=" N MET V 62 " --> pdb=" O ILE V 40 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL V 42 " --> pdb=" O MET V 60 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET V 60 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA V 102 " --> pdb=" O ILE V 82 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLY V 103 " --> pdb=" O VAL V 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN V 27 " --> pdb=" O GLY V 103 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE V 105 " --> pdb=" O ASN V 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 88 through 89 removed outlier: 3.537A pdb=" N LEU V 96 " --> pdb=" O TYR V 88 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE V 95 " --> pdb=" O ARG W 20 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ALA W 22 " --> pdb=" O PHE V 95 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR V 97 " --> pdb=" O ALA W 22 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 4 through 5 Processing sheet with id=AH3, first strand: chain 'X' and resid 77 through 80 removed outlier: 6.989A pdb=" N ILE X 99 " --> pdb=" O LYS X 78 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL X 97 " --> pdb=" O PRO X 80 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS X 134 " --> pdb=" O VAL X 100 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS X 123 " --> pdb=" O ARG X 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AH5, first strand: chain 'Y' and resid 79 through 82 removed outlier: 7.366A pdb=" N VAL Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL Y 73 " --> pdb=" O VAL Y 79 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR Y 81 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AH7, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.426A pdb=" N LYS Z 69 " --> pdb=" O ASP Z 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY Z 45 " --> pdb=" O PHE Z 71 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS Z 73 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL Z 43 " --> pdb=" O LYS Z 73 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA Z 41 " --> pdb=" O TYR Z 75 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N HIS Z 40 " --> pdb=" O ASN Z 28 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN Z 28 " --> pdb=" O HIS Z 40 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE Z 46 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 72 through 74 removed outlier: 6.291A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'a' and resid 100 through 102 removed outlier: 6.315A pdb=" N VAL a 124 " --> pdb=" O VAL a 145 " (cutoff:3.500A) 1996 hydrogen bonds defined for protein. 5595 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3053 hydrogen bonds 5214 hydrogen bond angles 0 basepair planarities 1169 basepair parallelities 1781 stacking parallelities Total time for adding SS restraints: 243.22 Time building geometry restraints manager: 56.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22725 1.33 - 1.45: 56069 1.45 - 1.57: 58313 1.57 - 1.69: 7517 1.69 - 1.81: 381 Bond restraints: 145005 Sorted by residual: bond pdb=" C ASN u 76 " pdb=" O ASN u 76 " ideal model delta sigma weight residual 1.235 1.246 -0.012 4.70e-03 4.53e+04 6.00e+00 bond pdb=" CB ASP k 30 " pdb=" CG ASP k 30 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.58e+00 bond pdb=" C3' A 55061 " pdb=" O3' A 55061 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.53e+00 bond pdb=" C VAL G 128 " pdb=" N PRO G 129 " ideal model delta sigma weight residual 1.333 1.345 -0.012 7.80e-03 1.64e+04 2.30e+00 bond pdb=" C LYS k 29 " pdb=" N ASP k 30 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.36e-02 5.41e+03 1.91e+00 ... (remaining 145000 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.29: 22368 106.29 - 113.22: 83853 113.22 - 120.14: 51938 120.14 - 127.07: 47050 127.07 - 134.00: 8765 Bond angle restraints: 213974 Sorted by residual: angle pdb=" N VAL G 168 " pdb=" CA VAL G 168 " pdb=" C VAL G 168 " ideal model delta sigma weight residual 113.71 107.69 6.02 9.50e-01 1.11e+00 4.01e+01 angle pdb=" C3' A 55061 " pdb=" O3' A 55061 " pdb=" P G 55062 " ideal model delta sigma weight residual 120.20 128.02 -7.82 1.50e+00 4.44e-01 2.72e+01 angle pdb=" N ASN k 31 " pdb=" CA ASN k 31 " pdb=" C ASN k 31 " ideal model delta sigma weight residual 110.61 104.39 6.22 1.25e+00 6.40e-01 2.47e+01 angle pdb=" N ILE H 41 " pdb=" CA ILE H 41 " pdb=" C ILE H 41 " ideal model delta sigma weight residual 113.71 109.25 4.46 9.50e-01 1.11e+00 2.20e+01 angle pdb=" O3' A 55061 " pdb=" C3' A 55061 " pdb=" C2' A 55061 " ideal model delta sigma weight residual 109.50 115.96 -6.46 1.50e+00 4.44e-01 1.86e+01 ... (remaining 213969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 83610 35.99 - 71.97: 8956 71.97 - 107.96: 1266 107.96 - 143.95: 31 143.95 - 179.93: 85 Dihedral angle restraints: 93948 sinusoidal: 74728 harmonic: 19220 Sorted by residual: dihedral pdb=" O4' C 54413 " pdb=" C1' C 54413 " pdb=" N1 C 54413 " pdb=" C2 C 54413 " ideal model delta sinusoidal sigma weight residual -160.00 16.86 -176.86 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 54423 " pdb=" C1' U 54423 " pdb=" N1 U 54423 " pdb=" C2 U 54423 " ideal model delta sinusoidal sigma weight residual -160.00 14.72 -174.72 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U 52097 " pdb=" C1' U 52097 " pdb=" N1 U 52097 " pdb=" C2 U 52097 " ideal model delta sinusoidal sigma weight residual -160.00 13.49 -173.49 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 93945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 24139 0.045 - 0.091: 1935 0.091 - 0.136: 559 0.136 - 0.181: 42 0.181 - 0.226: 12 Chirality restraints: 26687 Sorted by residual: chirality pdb=" P G 55062 " pdb=" OP1 G 55062 " pdb=" OP2 G 55062 " pdb=" O5' G 55062 " both_signs ideal model delta sigma weight residual True 2.41 -2.64 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' U 54888 " pdb=" C4' U 54888 " pdb=" O3' U 54888 " pdb=" C2' U 54888 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C3' A 55061 " pdb=" C4' A 55061 " pdb=" O3' A 55061 " pdb=" C2' A 55061 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 26684 not shown) Planarity restraints: 13041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR f 106 " -0.050 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO f 107 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO f 107 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO f 107 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U 5 370 " -0.030 2.00e-02 2.50e+03 1.57e-02 5.52e+00 pdb=" N1 U 5 370 " 0.034 2.00e-02 2.50e+03 pdb=" C2 U 5 370 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U 5 370 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U 5 370 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U 5 370 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U 5 370 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U 5 370 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U 5 370 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO O 109 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO O 110 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO O 110 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO O 110 " 0.032 5.00e-02 4.00e+02 ... (remaining 13038 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 2936 2.62 - 3.19: 107651 3.19 - 3.76: 254762 3.76 - 4.33: 339981 4.33 - 4.90: 478786 Nonbonded interactions: 1184116 Sorted by model distance: nonbonded pdb=" O6 G 51321 " pdb="MG MG 55194 " model vdw 2.054 2.170 nonbonded pdb=" OP2 C 51521 " pdb="MG MG 55105 " model vdw 2.054 2.170 nonbonded pdb=" OP1 A 54394 " pdb="MG MG 55194 " model vdw 2.056 2.170 nonbonded pdb=" OP1 C 5 112 " pdb="MG MG 55120 " model vdw 2.062 2.170 nonbonded pdb=" OP1 C 52794 " pdb="MG MG 55155 " model vdw 2.077 2.170 ... (remaining 1184111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 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: 0.120 Extract box with map and model: 22.940 Check model and map are aligned: 1.430 Set scattering table: 0.920 Process input model: 495.670 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 539.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 145005 Z= 0.103 Angle : 0.466 10.975 213974 Z= 0.242 Chirality : 0.028 0.226 26687 Planarity : 0.003 0.077 13041 Dihedral : 22.873 179.932 81554 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 0.72 % Allowed : 3.15 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.10), residues: 6529 helix: 1.00 (0.12), residues: 2126 sheet: -0.53 (0.18), residues: 890 loop : -1.28 (0.10), residues: 3513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 35 HIS 0.007 0.001 HIS G 195 PHE 0.010 0.001 PHE M 64 TYR 0.013 0.001 TYR D 44 ARG 0.004 0.000 ARG J 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1543 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1502 time to evaluate : 6.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 55 ASN cc_start: -0.0965 (OUTLIER) cc_final: -0.1468 (t0) REVERT: A 76 PHE cc_start: 0.6660 (m-10) cc_final: 0.6061 (m-80) REVERT: b 40 LEU cc_start: 0.6624 (mm) cc_final: 0.6156 (mt) REVERT: B 292 LEU cc_start: 0.6357 (pt) cc_final: 0.5776 (tp) REVERT: B 369 ASP cc_start: 0.6092 (t70) cc_final: 0.5852 (t70) REVERT: c 42 LYS cc_start: 0.5207 (mmtm) cc_final: 0.4819 (mtmm) REVERT: C 10 VAL cc_start: 0.8051 (m) cc_final: 0.7738 (t) REVERT: C 101 MET cc_start: 0.8597 (ptm) cc_final: 0.8199 (ptp) REVERT: D 155 THR cc_start: 0.6864 (m) cc_final: 0.6611 (m) REVERT: D 270 LYS cc_start: 0.5571 (mmmt) cc_final: 0.5259 (tppt) REVERT: E 163 GLN cc_start: 0.6717 (tt0) cc_final: 0.6496 (tt0) REVERT: F 222 MET cc_start: 0.5282 (mtp) cc_final: 0.4984 (mtt) REVERT: G 109 GLU cc_start: 0.3101 (OUTLIER) cc_final: 0.2664 (mp0) REVERT: G 153 GLN cc_start: 0.4982 (tm-30) cc_final: 0.4044 (mt0) REVERT: h 3 LYS cc_start: 0.4450 (OUTLIER) cc_final: 0.3705 (tttm) REVERT: h 59 THR cc_start: 0.8052 (m) cc_final: 0.7804 (m) REVERT: H 39 ASN cc_start: 0.6208 (m-40) cc_final: 0.5939 (m-40) REVERT: i 32 ARG cc_start: 0.6245 (mmm160) cc_final: 0.5984 (mmm-85) REVERT: I 11 TYR cc_start: 0.7632 (m-10) cc_final: 0.7235 (m-80) REVERT: J 12 MET cc_start: 0.6020 (mpp) cc_final: 0.5814 (mmm) REVERT: L 17 ASP cc_start: 0.7871 (t0) cc_final: 0.7615 (t70) REVERT: M 3 PHE cc_start: 0.7922 (m-80) cc_final: 0.7695 (m-80) REVERT: M 124 LYS cc_start: 0.5415 (mttt) cc_final: 0.4782 (tptp) REVERT: M 126 GLU cc_start: 0.3835 (tp30) cc_final: 0.3604 (mm-30) REVERT: O 132 THR cc_start: 0.7048 (m) cc_final: 0.6757 (t) REVERT: O 144 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7558 (mt-10) REVERT: o 42 ASP cc_start: 0.7203 (m-30) cc_final: 0.6996 (m-30) REVERT: P 142 VAL cc_start: 0.7696 (m) cc_final: 0.7479 (t) REVERT: p 10 ILE cc_start: 0.7774 (tp) cc_final: 0.7523 (tt) REVERT: S 64 CYS cc_start: 0.5755 (t) cc_final: 0.5553 (t) REVERT: T 65 TYR cc_start: 0.8515 (p90) cc_final: 0.8282 (p90) REVERT: T 143 THR cc_start: 0.5240 (OUTLIER) cc_final: 0.5000 (t) REVERT: U 95 ASN cc_start: 0.6586 (t0) cc_final: 0.6091 (m-40) REVERT: U 109 SER cc_start: 0.7540 (t) cc_final: 0.7247 (t) REVERT: U 112 LEU cc_start: 0.7524 (mp) cc_final: 0.7315 (mp) REVERT: Y 20 ASN cc_start: 0.7875 (m110) cc_final: 0.7625 (m110) REVERT: Y 72 GLN cc_start: 0.7381 (pt0) cc_final: 0.7092 (pt0) REVERT: a 58 MET cc_start: 0.8087 (mtm) cc_final: 0.7612 (mtp) REVERT: a 116 LYS cc_start: 0.5938 (ttpp) cc_final: 0.4829 (mmtp) outliers start: 41 outliers final: 17 residues processed: 1526 average time/residue: 2.2325 time to fit residues: 4710.0115 Evaluate side-chains 892 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 871 time to evaluate : 6.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain P residue 178 ILE Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 96 LEU Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain Z residue 62 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 861 optimal weight: 10.0000 chunk 773 optimal weight: 50.0000 chunk 428 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 521 optimal weight: 0.0970 chunk 413 optimal weight: 20.0000 chunk 799 optimal weight: 20.0000 chunk 309 optimal weight: 20.0000 chunk 486 optimal weight: 5.9990 chunk 595 optimal weight: 20.0000 chunk 926 optimal weight: 20.0000 overall best weight: 6.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 15 GLN u 17 GLN A 50 HIS A 95 GLN A 132 ASN A 139 HIS b 61 ASN B 55 HIS B 184 GLN B 186 ASN B 209 GLN B 276 HIS B 289 GLN B 380 GLN C 38 ASN C 41 HIS C 142 HIS C 212 ASN C 245 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN d 118 GLN D 45 ASN D 63 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 GLN e 24 GLN e 52 GLN ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 56 ASN F 82 ASN F 121 ASN F 207 ASN F 208 ASN F 243 ASN g 28 ASN G 64 GLN G 66 GLN G 100 HIS ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 ASN G 227 ASN h 30 GLN h 63 GLN h 98 HIS H 42 ASN H 76 HIS H 79 ASN H 163 GLN i 15 HIS I 59 GLN I 130 HIS J 42 GLN J 65 ASN J 71 HIS J 97 ASN J 98 ASN L 28 GLN L 87 HIS L 149 GLN l 17 GLN l 19 GLN l 33 ASN m 119 ASN N 87 HIS N 117 ASN O 96 GLN o 36 GLN P 50 ASN P 54 HIS P 104 GLN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 ASN ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 HIS p 72 ASN Q 160 HIS Q 188 ASN r 45 HIS r 121 GLN R 7 GLN R 58 HIS R 66 ASN S 91 HIS S 108 GLN S 144 GLN T 49 GLN T 54 HIS T 70 HIS T 77 ASN T 79 GLN U 105 ASN U 119 GLN V 101 ASN W 50 ASN ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 94 ASN X 125 ASN Y 4 ASN Y 24 HIS Z 97 ASN a 28 HIS a 66 ASN a 120 GLN Total number of N/Q/H flips: 97 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 145005 Z= 0.330 Angle : 0.802 17.209 213974 Z= 0.402 Chirality : 0.043 0.473 26687 Planarity : 0.007 0.095 13041 Dihedral : 24.475 179.446 67388 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.21 % Rotamer: Outliers : 5.81 % Allowed : 13.72 % Favored : 80.47 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % 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: -0.99 (0.10), residues: 6529 helix: 0.44 (0.11), residues: 2184 sheet: -0.69 (0.17), residues: 878 loop : -1.38 (0.10), residues: 3467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP p 55 HIS 0.015 0.002 HIS T 70 PHE 0.035 0.003 PHE B 150 TYR 0.035 0.003 TYR E 59 ARG 0.103 0.002 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1166 time to evaluate : 6.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: t 80 MET cc_start: 0.0620 (mpp) cc_final: 0.0104 (ttm) REVERT: u 6 MET cc_start: 0.6010 (mmm) cc_final: 0.5728 (mmm) REVERT: A 125 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7599 (mmtt) REVERT: A 193 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.6207 (mpp-170) REVERT: B 55 HIS cc_start: 0.5208 (m-70) cc_final: 0.4692 (m-70) REVERT: B 193 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7615 (mttt) REVERT: B 292 LEU cc_start: 0.7022 (pt) cc_final: 0.6455 (tp) REVERT: c 57 LYS cc_start: 0.7511 (ttpt) cc_final: 0.7208 (tttp) REVERT: C 10 VAL cc_start: 0.8521 (m) cc_final: 0.8211 (t) REVERT: C 61 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: C 290 SER cc_start: 0.8503 (t) cc_final: 0.8279 (p) REVERT: C 306 ARG cc_start: 0.6997 (mtm110) cc_final: 0.6783 (mtp180) REVERT: d 54 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.5637 (tmm) REVERT: d 67 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7047 (mtt90) REVERT: d 102 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8197 (pp) REVERT: D 133 GLU cc_start: 0.4282 (OUTLIER) cc_final: 0.3741 (pp20) REVERT: D 178 LYS cc_start: 0.7335 (tttt) cc_final: 0.6800 (ttmt) REVERT: D 225 GLN cc_start: 0.6626 (mm-40) cc_final: 0.5036 (mp10) REVERT: e 14 LYS cc_start: 0.7931 (mttm) cc_final: 0.7636 (mtpp) REVERT: E 258 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6223 (ptmt) REVERT: F 112 GLN cc_start: 0.7660 (pt0) cc_final: 0.7398 (mt0) REVERT: F 201 LYS cc_start: 0.7753 (mmtt) cc_final: 0.7231 (mtmt) REVERT: G 109 GLU cc_start: 0.4066 (pm20) cc_final: 0.3772 (pm20) REVERT: h 3 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.4050 (tttp) REVERT: h 71 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7577 (ttmm) REVERT: H 7 ASN cc_start: 0.6258 (p0) cc_final: 0.5965 (p0) REVERT: H 8 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: H 70 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7523 (t) REVERT: i 38 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7624 (tttp) REVERT: i 84 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6798 (tttt) REVERT: I 11 TYR cc_start: 0.8045 (m-10) cc_final: 0.7607 (m-80) REVERT: I 26 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7364 (t) REVERT: I 56 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: I 184 MET cc_start: 0.5360 (ttm) cc_final: 0.5096 (ttm) REVERT: j 72 ARG cc_start: 0.7848 (tmm160) cc_final: 0.7621 (tmm160) REVERT: J 12 MET cc_start: 0.6476 (mpp) cc_final: 0.5984 (mmm) REVERT: J 85 LYS cc_start: 0.5443 (OUTLIER) cc_final: 0.5061 (mttt) REVERT: J 88 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5574 (tttt) REVERT: J 113 ILE cc_start: 0.5765 (tp) cc_final: 0.5333 (tp) REVERT: k 3 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7750 (mpt90) REVERT: L 19 GLN cc_start: 0.7850 (mt0) cc_final: 0.7587 (mt0) REVERT: L 79 GLU cc_start: 0.6016 (tt0) cc_final: 0.5808 (tt0) REVERT: M 50 MET cc_start: 0.7225 (ptp) cc_final: 0.6776 (ptp) REVERT: M 57 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8276 (pp) REVERT: M 79 LYS cc_start: 0.5886 (tppp) cc_final: 0.5651 (mmmm) REVERT: M 124 LYS cc_start: 0.6042 (mttt) cc_final: 0.5390 (tptp) REVERT: M 126 GLU cc_start: 0.5195 (tp30) cc_final: 0.4988 (mm-30) REVERT: m 81 SER cc_start: 0.6857 (p) cc_final: 0.6473 (t) REVERT: N 38 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7062 (ttt180) REVERT: O 61 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7487 (ptt-90) REVERT: O 132 THR cc_start: 0.7223 (m) cc_final: 0.6983 (t) REVERT: O 144 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7925 (mt-10) REVERT: p 61 MET cc_start: 0.6835 (mmm) cc_final: 0.6338 (mmm) REVERT: p 78 THR cc_start: 0.8051 (m) cc_final: 0.7757 (m) REVERT: r 35 ARG cc_start: 0.8121 (ptp90) cc_final: 0.7901 (ptp-170) REVERT: r 80 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.6888 (t) REVERT: R 52 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7522 (ttp80) REVERT: R 96 MET cc_start: 0.8735 (ttm) cc_final: 0.8476 (ttm) REVERT: S 8 ARG cc_start: 0.7591 (ptm160) cc_final: 0.7379 (ptm160) REVERT: S 50 GLN cc_start: 0.7439 (tt0) cc_final: 0.7236 (tt0) REVERT: S 54 MET cc_start: 0.6875 (mtp) cc_final: 0.6589 (mtp) REVERT: S 64 CYS cc_start: 0.6251 (t) cc_final: 0.5943 (t) REVERT: T 87 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7577 (mtpp) REVERT: U 109 SER cc_start: 0.7563 (t) cc_final: 0.7358 (t) REVERT: U 119 GLN cc_start: 0.4009 (OUTLIER) cc_final: 0.3783 (pm20) REVERT: W 47 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.5972 (mtt-85) REVERT: X 41 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6050 (mtt-85) REVERT: Z 46 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.6115 (pt) REVERT: Z 60 LYS cc_start: 0.6234 (OUTLIER) cc_final: 0.5275 (mptm) REVERT: a 58 MET cc_start: 0.8382 (mtm) cc_final: 0.8079 (mtp) REVERT: a 64 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7878 (mtmt) outliers start: 330 outliers final: 104 residues processed: 1369 average time/residue: 2.1426 time to fit residues: 4106.4170 Evaluate side-chains 1025 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 889 time to evaluate : 6.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 258 LYS Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 99 LYS Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain k residue 3 ARG Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain o residue 25 GLN Chi-restraints excluded: chain o residue 67 VAL Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain p residue 48 LYS Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain r residue 120 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 52 ARG Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 127 MET Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain U residue 119 GLN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 91 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 55 ARG Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 93 LYS Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 514 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 chunk 770 optimal weight: 20.0000 chunk 630 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 927 optimal weight: 30.0000 chunk 1002 optimal weight: 6.9990 chunk 826 optimal weight: 20.0000 chunk 920 optimal weight: 9.9990 chunk 316 optimal weight: 30.0000 chunk 744 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 68 GLN b 17 HIS B 281 ASN C 317 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 81 HIS D 122 GLN ** D 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 102 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 HIS f 21 GLN f 80 ASN g 28 ASN G 64 GLN G 85 GLN G 90 GLN G 108 GLN G 141 ASN G 159 HIS G 227 ASN I 51 HIS I 86 HIS I 202 ASN I 213 HIS J 10 ASN l 4 HIS l 38 ASN M 20 HIS M 120 ASN m 84 GLN N 37 HIS ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 HIS r 30 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 22 HIS T 70 HIS T 139 HIS U 119 GLN W 48 GLN ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Y 72 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.200 145005 Z= 0.369 Angle : 0.810 20.791 213974 Z= 0.407 Chirality : 0.045 0.401 26687 Planarity : 0.007 0.106 13041 Dihedral : 24.617 179.977 67369 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.12 % Rotamer: Outliers : 7.34 % Allowed : 17.00 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.10), residues: 6529 helix: 0.29 (0.11), residues: 2199 sheet: -0.62 (0.17), residues: 903 loop : -1.47 (0.10), residues: 3427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 209 HIS 0.015 0.002 HIS S 163 PHE 0.043 0.003 PHE Z 101 TYR 0.030 0.003 TYR Q 32 ARG 0.031 0.001 ARG H 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1447 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 1030 time to evaluate : 6.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6906 (ptm160) REVERT: A 74 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7374 (mm-30) REVERT: A 125 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7702 (mmtt) REVERT: B 24 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7540 (ptp-110) REVERT: B 240 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8253 (mt) REVERT: B 332 MET cc_start: 0.7870 (ttm) cc_final: 0.7567 (ttm) REVERT: B 345 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7438 (mt) REVERT: B 357 ARG cc_start: 0.7137 (mtt90) cc_final: 0.6908 (mtp85) REVERT: c 36 LYS cc_start: 0.7925 (tttp) cc_final: 0.7280 (tmtt) REVERT: c 38 ILE cc_start: 0.8216 (mt) cc_final: 0.7852 (mt) REVERT: c 44 LYS cc_start: 0.6999 (mttm) cc_final: 0.6703 (mppt) REVERT: c 57 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7322 (tttp) REVERT: c 61 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6778 (mt-10) REVERT: c 80 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7199 (mt-10) REVERT: C 10 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8193 (t) REVERT: C 20 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.5784 (mmmt) REVERT: C 61 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: d 54 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.5694 (tmm) REVERT: d 67 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7070 (mtt90) REVERT: D 74 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7517 (mt) REVERT: D 76 CYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6716 (t) REVERT: D 210 TYR cc_start: 0.5629 (t80) cc_final: 0.5095 (t80) REVERT: D 225 GLN cc_start: 0.7050 (mm-40) cc_final: 0.5290 (mp10) REVERT: E 115 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6478 (pp20) REVERT: E 148 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7304 (mt) REVERT: E 185 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7743 (p) REVERT: E 258 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6595 (ptpt) REVERT: F 32 ILE cc_start: 0.5908 (mm) cc_final: 0.5427 (mp) REVERT: F 64 ARG cc_start: 0.7664 (tmm-80) cc_final: 0.7217 (ttp-110) REVERT: F 112 GLN cc_start: 0.7754 (pt0) cc_final: 0.7282 (mt0) REVERT: F 132 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7772 (mp) REVERT: F 183 LYS cc_start: 0.7530 (ptmt) cc_final: 0.7290 (ptmt) REVERT: F 202 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6754 (mpt-90) REVERT: g 3 GLN cc_start: 0.7131 (pt0) cc_final: 0.6900 (pt0) REVERT: G 46 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7519 (mp10) REVERT: G 109 GLU cc_start: 0.4372 (pm20) cc_final: 0.3816 (pm20) REVERT: G 220 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.5027 (mp0) REVERT: h 7 ARG cc_start: 0.6096 (mtp180) cc_final: 0.5863 (ptp-170) REVERT: h 18 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7427 (mp) REVERT: h 32 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7089 (mtt-85) REVERT: h 43 LYS cc_start: 0.7220 (mtpp) cc_final: 0.6701 (mtpt) REVERT: H 12 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7376 (pt) REVERT: H 28 LYS cc_start: 0.7847 (tmmt) cc_final: 0.7463 (ttpp) REVERT: H 39 ASN cc_start: 0.7200 (m-40) cc_final: 0.6922 (m-40) REVERT: H 78 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7715 (tp40) REVERT: i 38 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7306 (tptt) REVERT: i 84 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7112 (ptmt) REVERT: i 99 LYS cc_start: 0.5121 (OUTLIER) cc_final: 0.4697 (tppp) REVERT: I 56 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: j 73 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7519 (ttm170) REVERT: J 113 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5571 (tp) REVERT: k 30 ASP cc_start: 0.6117 (OUTLIER) cc_final: 0.5637 (m-30) REVERT: L 108 GLU cc_start: 0.8013 (mp0) cc_final: 0.7795 (mp0) REVERT: L 190 ARG cc_start: 0.7106 (ttp-110) cc_final: 0.6789 (ttt180) REVERT: L 195 ARG cc_start: 0.6946 (ttm110) cc_final: 0.6559 (mtm180) REVERT: l 28 ARG cc_start: 0.7313 (mtp180) cc_final: 0.7098 (mtp180) REVERT: M 57 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8242 (pp) REVERT: M 61 ILE cc_start: 0.7951 (mt) cc_final: 0.7710 (mt) REVERT: M 124 LYS cc_start: 0.6592 (mttt) cc_final: 0.6145 (tptp) REVERT: m 82 LEU cc_start: 0.7781 (mm) cc_final: 0.7375 (mt) REVERT: m 98 LYS cc_start: 0.7215 (mttt) cc_final: 0.6924 (mttm) REVERT: N 10 LEU cc_start: 0.7101 (mt) cc_final: 0.6699 (mt) REVERT: N 161 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6818 (mpt) REVERT: O 61 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7541 (ptt-90) REVERT: O 132 THR cc_start: 0.7326 (m) cc_final: 0.7082 (t) REVERT: O 191 ARG cc_start: 0.6407 (OUTLIER) cc_final: 0.6189 (mtp-110) REVERT: o 28 LYS cc_start: 0.7533 (tptm) cc_final: 0.7168 (ttmp) REVERT: o 71 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6491 (pt0) REVERT: o 87 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8436 (ptm160) REVERT: P 133 LEU cc_start: 0.8138 (tm) cc_final: 0.7926 (tm) REVERT: P 155 ARG cc_start: 0.7617 (ptp-110) cc_final: 0.7334 (ttm-80) REVERT: p 10 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7939 (tp) REVERT: p 61 MET cc_start: 0.7517 (mmm) cc_final: 0.7299 (mmm) REVERT: p 78 THR cc_start: 0.8121 (m) cc_final: 0.7868 (m) REVERT: r 101 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7457 (mttm) REVERT: r 125 MET cc_start: 0.1577 (tmm) cc_final: 0.1230 (tpt) REVERT: R 44 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8046 (tp) REVERT: R 52 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7542 (ttp80) REVERT: R 126 LYS cc_start: 0.8131 (mttm) cc_final: 0.7847 (mttt) REVERT: S 30 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7727 (mtm) REVERT: S 96 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: S 132 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7786 (mt) REVERT: T 14 MET cc_start: 0.7495 (ttm) cc_final: 0.6890 (ttm) REVERT: T 31 MET cc_start: 0.7811 (mtp) cc_final: 0.7359 (mtm) REVERT: T 87 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7215 (mtpp) REVERT: T 114 GLN cc_start: 0.4783 (tm-30) cc_final: 0.4546 (tm-30) REVERT: U 71 THR cc_start: 0.5812 (OUTLIER) cc_final: 0.5461 (t) REVERT: U 109 SER cc_start: 0.7715 (t) cc_final: 0.7495 (t) REVERT: U 116 GLN cc_start: 0.5902 (OUTLIER) cc_final: 0.4994 (tp40) REVERT: W 47 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6189 (mtt-85) REVERT: W 53 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8675 (t) REVERT: W 54 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8392 (mt) REVERT: X 41 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6206 (mtt-85) REVERT: X 87 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6534 (mpm) REVERT: Y 17 ARG cc_start: 0.7284 (ptp-110) cc_final: 0.6731 (ptp-170) REVERT: Z 57 MET cc_start: 0.2513 (pmt) cc_final: 0.2175 (pmm) REVERT: Z 60 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5692 (tppp) REVERT: a 116 LYS cc_start: 0.7335 (ttpp) cc_final: 0.6997 (pttt) outliers start: 417 outliers final: 173 residues processed: 1288 average time/residue: 2.1199 time to fit residues: 3820.0996 Evaluate side-chains 1070 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 847 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain c residue 21 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain e residue 91 CYS Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 258 LYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 18 LEU Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 37 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 99 LYS Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 82 THR Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 159 LYS Chi-restraints excluded: chain k residue 6 GLU Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain l residue 21 ARG Chi-restraints excluded: chain l residue 23 ILE Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain m residue 94 MET Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain o residue 25 GLN Chi-restraints excluded: chain o residue 67 VAL Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 48 LYS Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain r residue 120 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 52 ARG Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 116 GLN Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 114 ASP Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 140 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 916 optimal weight: 20.0000 chunk 697 optimal weight: 10.0000 chunk 481 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 442 optimal weight: 9.9990 chunk 623 optimal weight: 10.0000 chunk 931 optimal weight: 20.0000 chunk 985 optimal weight: 20.0000 chunk 486 optimal weight: 5.9990 chunk 882 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 45 GLN u 80 GLN B 281 ASN B 301 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 122 GLN e 102 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN g 28 ASN G 85 GLN G 225 ASN H 42 ASN H 162 GLN j 13 ASN L 188 ASN l 4 HIS N 29 GLN ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 145 ASN O 26 GLN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 6 GLN r 30 ASN R 36 ASN ** R 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 ASN W 50 ASN ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 145005 Z= 0.346 Angle : 0.785 24.399 213974 Z= 0.395 Chirality : 0.045 0.387 26687 Planarity : 0.007 0.091 13041 Dihedral : 24.563 179.752 67369 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 7.86 % Allowed : 18.75 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 6529 helix: 0.41 (0.11), residues: 2172 sheet: -0.69 (0.16), residues: 909 loop : -1.42 (0.10), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP p 55 HIS 0.032 0.002 HIS R 143 PHE 0.022 0.002 PHE Z 101 TYR 0.026 0.003 TYR t 120 ARG 0.012 0.001 ARG H 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 447 poor density : 912 time to evaluate : 6.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: A 125 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7697 (mmtt) REVERT: B 240 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8127 (mt) REVERT: B 315 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7258 (p0) REVERT: B 345 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7547 (mt) REVERT: B 354 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6473 (mp10) REVERT: c 17 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6925 (mtt90) REVERT: c 36 LYS cc_start: 0.8023 (tttp) cc_final: 0.7293 (tmtt) REVERT: c 38 ILE cc_start: 0.8207 (mt) cc_final: 0.7989 (mt) REVERT: c 57 LYS cc_start: 0.7718 (ttpt) cc_final: 0.7313 (tttp) REVERT: c 61 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6654 (mt-10) REVERT: c 78 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7244 (p0) REVERT: C 20 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5691 (mmmt) REVERT: C 61 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: C 147 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8315 (t) REVERT: C 230 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7767 (pp) REVERT: d 54 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.5690 (tmm) REVERT: d 63 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7231 (mtm-85) REVERT: d 67 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7074 (mtt90) REVERT: D 23 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7926 (tpt170) REVERT: D 74 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7550 (mt) REVERT: D 76 CYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6699 (m) REVERT: D 120 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.6128 (tt0) REVERT: D 237 GLU cc_start: 0.5959 (tt0) cc_final: 0.5640 (mp0) REVERT: E 115 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6483 (pp20) REVERT: E 148 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7171 (mt) REVERT: E 216 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.5990 (mttt) REVERT: E 258 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6753 (ptpt) REVERT: F 32 ILE cc_start: 0.6509 (mm) cc_final: 0.6117 (mp) REVERT: F 64 ARG cc_start: 0.7734 (tmm-80) cc_final: 0.7341 (ttp-110) REVERT: F 112 GLN cc_start: 0.7781 (pt0) cc_final: 0.7318 (mt0) REVERT: F 132 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7671 (mp) REVERT: F 202 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6821 (mpt-90) REVERT: G 46 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7590 (mp10) REVERT: G 64 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: G 109 GLU cc_start: 0.4554 (pm20) cc_final: 0.3911 (pm20) REVERT: G 115 LEU cc_start: 0.4822 (OUTLIER) cc_final: 0.4608 (pp) REVERT: G 220 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5383 (mp0) REVERT: h 7 ARG cc_start: 0.6143 (mtp180) cc_final: 0.5752 (ptp-170) REVERT: h 32 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7107 (mtt-85) REVERT: h 112 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.5989 (tmt90) REVERT: H 12 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7370 (pt) REVERT: H 28 LYS cc_start: 0.7746 (tmmt) cc_final: 0.7514 (ttpp) REVERT: H 39 ASN cc_start: 0.7169 (m-40) cc_final: 0.6832 (m-40) REVERT: H 72 THR cc_start: 0.8472 (p) cc_final: 0.8199 (m) REVERT: H 78 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7679 (tp40) REVERT: H 128 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6348 (mtp) REVERT: i 38 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7159 (tptt) REVERT: i 43 MET cc_start: 0.7421 (tpp) cc_final: 0.7175 (mmt) REVERT: i 84 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6976 (tttt) REVERT: i 99 LYS cc_start: 0.5477 (OUTLIER) cc_final: 0.5093 (ttpp) REVERT: I 26 VAL cc_start: 0.7998 (p) cc_final: 0.7413 (t) REVERT: I 35 ASP cc_start: 0.7578 (p0) cc_final: 0.7361 (p0) REVERT: I 162 ARG cc_start: 0.7408 (ttt90) cc_final: 0.6958 (ttt90) REVERT: J 113 ILE cc_start: 0.6183 (tp) cc_final: 0.5708 (tp) REVERT: k 6 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5999 (tp30) REVERT: k 13 LEU cc_start: 0.7446 (mp) cc_final: 0.6985 (tp) REVERT: L 74 ARG cc_start: 0.8534 (ttt90) cc_final: 0.8305 (ttt180) REVERT: L 164 GLU cc_start: 0.5695 (mp0) cc_final: 0.5255 (mm-30) REVERT: L 190 ARG cc_start: 0.7378 (ttp-110) cc_final: 0.7044 (ttt90) REVERT: L 195 ARG cc_start: 0.7055 (ttm110) cc_final: 0.6634 (mtm180) REVERT: M 57 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8071 (pp) REVERT: M 105 THR cc_start: 0.7266 (OUTLIER) cc_final: 0.7033 (m) REVERT: N 161 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6688 (mpt) REVERT: n 18 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.6886 (mtm110) REVERT: O 61 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7567 (ptt-90) REVERT: O 132 THR cc_start: 0.7402 (m) cc_final: 0.7127 (t) REVERT: o 25 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7738 (tp40) REVERT: o 28 LYS cc_start: 0.7531 (tptm) cc_final: 0.7254 (ttmp) REVERT: o 71 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6554 (pt0) REVERT: o 87 ARG cc_start: 0.8648 (ptp-110) cc_final: 0.8405 (ptm160) REVERT: P 104 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: P 155 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7317 (ttm-80) REVERT: p 10 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7876 (tp) REVERT: p 61 MET cc_start: 0.7476 (mmm) cc_final: 0.7186 (mmm) REVERT: p 78 THR cc_start: 0.8004 (m) cc_final: 0.7792 (m) REVERT: Q 150 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7643 (mtt180) REVERT: r 35 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7768 (ptp90) REVERT: r 101 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7483 (mttm) REVERT: r 125 MET cc_start: 0.1170 (tmm) cc_final: 0.0864 (tpt) REVERT: R 44 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7845 (tp) REVERT: R 52 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7345 (ttp80) REVERT: R 89 MET cc_start: 0.7975 (tpt) cc_final: 0.7643 (tpt) REVERT: R 126 LYS cc_start: 0.8134 (mttm) cc_final: 0.7917 (mttt) REVERT: S 96 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: T 14 MET cc_start: 0.7560 (ttm) cc_final: 0.6879 (ttm) REVERT: T 87 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7460 (mtpp) REVERT: T 114 GLN cc_start: 0.5075 (tm-30) cc_final: 0.4854 (tm-30) REVERT: T 122 LYS cc_start: 0.3162 (mmtp) cc_final: 0.1454 (tppt) REVERT: U 56 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3446 (tp) REVERT: U 109 SER cc_start: 0.7547 (t) cc_final: 0.7270 (t) REVERT: U 116 GLN cc_start: 0.6008 (OUTLIER) cc_final: 0.5612 (mp10) REVERT: W 28 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7658 (t) REVERT: W 47 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6113 (mtt-85) REVERT: X 41 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6326 (mtt-85) REVERT: X 87 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6528 (mpm) REVERT: X 156 ILE cc_start: 0.4921 (OUTLIER) cc_final: 0.4281 (mm) REVERT: Y 17 ARG cc_start: 0.7364 (ptp-110) cc_final: 0.6939 (ptp-170) REVERT: Z 57 MET cc_start: 0.2523 (pmt) cc_final: 0.2244 (pmm) REVERT: Z 60 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5710 (tppp) REVERT: Z 62 ILE cc_start: 0.8035 (mt) cc_final: 0.7756 (mt) outliers start: 447 outliers final: 212 residues processed: 1204 average time/residue: 2.1416 time to fit residues: 3625.1987 Evaluate side-chains 1118 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 846 time to evaluate : 6.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 63 ARG Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 91 CYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 258 LYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 88 ARG Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 112 ARG Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 99 LYS Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 82 THR Chi-restraints excluded: chain k residue 6 GLU Chi-restraints excluded: chain k residue 18 LYS Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain l residue 21 ARG Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 170 LYS Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain o residue 25 GLN Chi-restraints excluded: chain o residue 67 VAL Chi-restraints excluded: chain o residue 71 GLU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 155 ARG Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 38 THR Chi-restraints excluded: chain p residue 48 LYS Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 35 ARG Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain r residue 120 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 52 ARG Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 116 GLN Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain V residue 108 ASN Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 134 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 156 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 821 optimal weight: 10.0000 chunk 559 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 734 optimal weight: 9.9990 chunk 406 optimal weight: 5.9990 chunk 841 optimal weight: 10.0000 chunk 681 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 503 optimal weight: 10.0000 chunk 884 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 222 GLN D 267 ASN D 275 GLN e 57 ASN e 102 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN G 82 GLN H 15 ASN I 144 ASN j 13 ASN ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 HIS l 25 GLN N 29 GLN N 37 HIS N 87 HIS o 90 HIS P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 ASN P 130 ASN P 166 ASN ** Q 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 HIS W 50 ASN ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 151 ASN Y 127 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 145005 Z= 0.322 Angle : 0.761 24.983 213974 Z= 0.383 Chirality : 0.043 0.377 26687 Planarity : 0.006 0.092 13041 Dihedral : 24.558 179.888 67369 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.96 % Favored : 94.03 % Rotamer: Outliers : 7.86 % Allowed : 19.90 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.10), residues: 6529 helix: 0.51 (0.11), residues: 2177 sheet: -0.55 (0.16), residues: 906 loop : -1.43 (0.10), residues: 3446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP j 49 HIS 0.011 0.002 HIS a 40 PHE 0.020 0.002 PHE Q 174 TYR 0.026 0.002 TYR D 44 ARG 0.015 0.001 ARG O 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 447 poor density : 863 time to evaluate : 6.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: A 125 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7679 (mmtt) REVERT: B 24 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7728 (ptp-110) REVERT: B 240 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8187 (mt) REVERT: B 345 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7491 (mt) REVERT: B 354 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6487 (mp10) REVERT: c 38 ILE cc_start: 0.8130 (mt) cc_final: 0.7819 (mt) REVERT: c 40 GLN cc_start: 0.7360 (tp40) cc_final: 0.6892 (mt0) REVERT: c 48 LEU cc_start: 0.8197 (mt) cc_final: 0.7988 (mt) REVERT: c 57 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7326 (tttp) REVERT: c 61 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6632 (mt-10) REVERT: c 103 ASP cc_start: 0.6317 (m-30) cc_final: 0.5894 (t0) REVERT: C 20 LYS cc_start: 0.6448 (OUTLIER) cc_final: 0.5924 (mmmt) REVERT: C 61 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: C 147 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8297 (t) REVERT: C 230 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7725 (pp) REVERT: d 54 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.5656 (tmm) REVERT: d 63 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7222 (mtm-85) REVERT: d 67 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7067 (mtt90) REVERT: D 23 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8084 (tpt170) REVERT: D 76 CYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6809 (m) REVERT: D 85 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7242 (tptp) REVERT: D 104 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7417 (mt) REVERT: D 117 LYS cc_start: 0.7304 (mmmt) cc_final: 0.7015 (mmmm) REVERT: D 210 TYR cc_start: 0.5640 (t80) cc_final: 0.5102 (t80) REVERT: D 237 GLU cc_start: 0.5829 (tt0) cc_final: 0.5581 (mp0) REVERT: E 115 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6498 (pp20) REVERT: E 148 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7254 (mt) REVERT: E 216 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5833 (mttt) REVERT: F 32 ILE cc_start: 0.6750 (mm) cc_final: 0.6405 (mp) REVERT: F 64 ARG cc_start: 0.7724 (tmm-80) cc_final: 0.7337 (ttp-110) REVERT: F 112 GLN cc_start: 0.7818 (pt0) cc_final: 0.7395 (mt0) REVERT: F 132 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7725 (mp) REVERT: F 202 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6815 (mpt-90) REVERT: F 239 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: G 46 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7538 (mp10) REVERT: G 109 GLU cc_start: 0.4647 (pm20) cc_final: 0.4242 (pm20) REVERT: G 115 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4767 (pp) REVERT: G 220 GLU cc_start: 0.5779 (OUTLIER) cc_final: 0.5309 (mp0) REVERT: h 7 ARG cc_start: 0.6138 (mtp180) cc_final: 0.5795 (ptp-170) REVERT: h 32 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7064 (mtt-85) REVERT: h 112 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.6078 (tmt90) REVERT: H 12 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7440 (pt) REVERT: H 28 LYS cc_start: 0.7628 (tmmt) cc_final: 0.7108 (tttp) REVERT: H 39 ASN cc_start: 0.7039 (m-40) cc_final: 0.6747 (m-40) REVERT: H 78 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7675 (tp40) REVERT: H 128 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6129 (mtp) REVERT: i 38 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7093 (tptt) REVERT: i 84 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.7023 (tttt) REVERT: i 99 LYS cc_start: 0.5721 (OUTLIER) cc_final: 0.5290 (tppp) REVERT: I 44 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6744 (p0) REVERT: I 209 TRP cc_start: 0.7581 (t60) cc_final: 0.7263 (t60) REVERT: J 33 LEU cc_start: 0.6560 (tp) cc_final: 0.6359 (tp) REVERT: J 113 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.5631 (tp) REVERT: J 175 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5477 (pt) REVERT: k 6 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5824 (tp30) REVERT: L 31 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7979 (ttm110) REVERT: L 190 ARG cc_start: 0.7374 (ttp-110) cc_final: 0.7097 (ttt90) REVERT: L 195 ARG cc_start: 0.7118 (ttm110) cc_final: 0.6641 (mtm180) REVERT: l 28 ARG cc_start: 0.7285 (mtp180) cc_final: 0.7055 (mtp180) REVERT: M 57 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8029 (pp) REVERT: N 96 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7270 (ttp80) REVERT: N 161 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6693 (mpt) REVERT: n 18 ARG cc_start: 0.7180 (mtm-85) cc_final: 0.6745 (mtm110) REVERT: O 49 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6750 (ptm-80) REVERT: O 61 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7536 (ptt-90) REVERT: O 112 TYR cc_start: 0.7556 (m-80) cc_final: 0.7221 (m-80) REVERT: O 132 THR cc_start: 0.7479 (m) cc_final: 0.7164 (t) REVERT: o 25 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7637 (tp40) REVERT: o 28 LYS cc_start: 0.7493 (tptm) cc_final: 0.7226 (ttmp) REVERT: o 87 ARG cc_start: 0.8632 (ptp-110) cc_final: 0.8288 (ptm160) REVERT: P 104 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: P 155 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7370 (ttm-80) REVERT: p 10 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7981 (tp) REVERT: p 61 MET cc_start: 0.7591 (mmm) cc_final: 0.7321 (mmm) REVERT: p 78 THR cc_start: 0.7992 (m) cc_final: 0.7766 (m) REVERT: Q 150 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7626 (mtt180) REVERT: r 101 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7567 (mttm) REVERT: r 125 MET cc_start: 0.1310 (tmm) cc_final: 0.1071 (tpt) REVERT: R 44 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7751 (tp) REVERT: R 52 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7415 (ttp80) REVERT: R 89 MET cc_start: 0.7948 (tpt) cc_final: 0.7623 (tpt) REVERT: R 135 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.8007 (mtmt) REVERT: R 151 ARG cc_start: 0.6929 (tpt170) cc_final: 0.6339 (tpp80) REVERT: R 154 LEU cc_start: 0.7584 (tm) cc_final: 0.7092 (tt) REVERT: R 158 GLN cc_start: 0.5319 (tm-30) cc_final: 0.4918 (tt0) REVERT: S 132 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7822 (pt) REVERT: T 14 MET cc_start: 0.7537 (ttm) cc_final: 0.6966 (ttm) REVERT: T 87 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7407 (mtpp) REVERT: T 122 LYS cc_start: 0.3373 (mmtp) cc_final: 0.1570 (tppt) REVERT: U 109 SER cc_start: 0.7592 (t) cc_final: 0.7317 (t) REVERT: U 116 GLN cc_start: 0.5975 (OUTLIER) cc_final: 0.5613 (mp10) REVERT: V 97 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7242 (p90) REVERT: V 109 LYS cc_start: 0.7458 (mtmt) cc_final: 0.7116 (mtpt) REVERT: W 28 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7688 (t) REVERT: W 47 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.5980 (mtt-85) REVERT: W 57 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.7228 (ttm-80) REVERT: X 40 ILE cc_start: 0.6376 (pt) cc_final: 0.6116 (pt) REVERT: X 41 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6602 (mtt-85) REVERT: X 87 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6578 (mpm) REVERT: X 151 ASN cc_start: 0.6582 (m110) cc_final: 0.6239 (m-40) REVERT: Y 17 ARG cc_start: 0.7393 (ptp-110) cc_final: 0.7035 (ptp-170) REVERT: Z 9 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7355 (tttp) REVERT: Z 57 MET cc_start: 0.2657 (pmt) cc_final: 0.2319 (pmm) REVERT: a 89 ASN cc_start: 0.7752 (m-40) cc_final: 0.7516 (m110) outliers start: 447 outliers final: 238 residues processed: 1163 average time/residue: 2.1361 time to fit residues: 3499.9349 Evaluate side-chains 1112 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 815 time to evaluate : 6.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 88 VAL Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain b residue 31 SER Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 63 ARG Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 57 ASN Chi-restraints excluded: chain e residue 91 CYS Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 88 ARG Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 18 LEU Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 112 ARG Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain i residue 99 LYS Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 82 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain k residue 6 GLU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 21 ARG Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 179 LYS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 170 LYS Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 25 GLN Chi-restraints excluded: chain o residue 67 VAL Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 155 ARG Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 38 THR Chi-restraints excluded: chain p residue 48 LYS Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain r residue 120 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 52 ARG Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 135 LYS Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 116 GLN Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 97 TYR Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 108 ASN Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 134 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 43 SER Chi-restraints excluded: chain X residue 77 ILE Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 140 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 331 optimal weight: 5.9990 chunk 887 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 578 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 986 optimal weight: 20.0000 chunk 819 optimal weight: 20.0000 chunk 456 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 518 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 175 HIS D 222 GLN D 267 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN J 71 HIS ** k 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 GLN N 29 GLN N 87 HIS o 90 HIS ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 95 ASN ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 145005 Z= 0.308 Angle : 0.750 27.518 213974 Z= 0.378 Chirality : 0.043 0.370 26687 Planarity : 0.006 0.108 13041 Dihedral : 24.546 179.844 67368 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.03 % Rotamer: Outliers : 8.00 % Allowed : 20.37 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.10), residues: 6529 helix: 0.60 (0.11), residues: 2181 sheet: -0.59 (0.16), residues: 930 loop : -1.42 (0.10), residues: 3418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP j 49 HIS 0.011 0.002 HIS S 163 PHE 0.020 0.002 PHE D 287 TYR 0.027 0.002 TYR D 44 ARG 0.018 0.001 ARG O 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 455 poor density : 846 time to evaluate : 6.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 64 MET cc_start: 0.2256 (ppp) cc_final: 0.2002 (pmm) REVERT: A 36 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: A 74 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: A 93 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7513 (mtpm) REVERT: b 65 MET cc_start: 0.5104 (tmm) cc_final: 0.3603 (mmt) REVERT: B 24 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7711 (ptp-110) REVERT: B 240 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8125 (mt) REVERT: B 345 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7596 (mt) REVERT: B 354 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6455 (mp10) REVERT: B 357 ARG cc_start: 0.7015 (mtt90) cc_final: 0.6800 (mtp85) REVERT: c 38 ILE cc_start: 0.8178 (mt) cc_final: 0.7896 (mt) REVERT: c 40 GLN cc_start: 0.7420 (tp40) cc_final: 0.6861 (mt0) REVERT: c 57 LYS cc_start: 0.7773 (ttpt) cc_final: 0.7306 (tttp) REVERT: c 61 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6637 (mt-10) REVERT: c 78 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7119 (p0) REVERT: c 103 ASP cc_start: 0.6432 (m-30) cc_final: 0.6059 (t0) REVERT: C 61 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: C 147 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8356 (t) REVERT: C 230 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7770 (pp) REVERT: d 51 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7430 (mtpm) REVERT: d 54 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.5613 (tmm) REVERT: d 63 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7203 (mtm-85) REVERT: d 67 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7076 (mtt90) REVERT: D 23 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8147 (tpt170) REVERT: D 85 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7155 (tptp) REVERT: D 210 TYR cc_start: 0.5598 (t80) cc_final: 0.4724 (t80) REVERT: D 237 GLU cc_start: 0.5724 (tt0) cc_final: 0.5513 (mp0) REVERT: e 32 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: e 128 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.5666 (ttm170) REVERT: E 115 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6543 (pp20) REVERT: E 148 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7257 (mt) REVERT: E 216 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.5958 (mttt) REVERT: F 32 ILE cc_start: 0.6606 (mm) cc_final: 0.6378 (mp) REVERT: F 64 ARG cc_start: 0.7729 (tmm-80) cc_final: 0.7362 (ttp-110) REVERT: F 112 GLN cc_start: 0.7803 (pt0) cc_final: 0.7367 (mt0) REVERT: F 132 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7690 (mp) REVERT: F 179 ARG cc_start: 0.6629 (mtt-85) cc_final: 0.6399 (mtt-85) REVERT: F 202 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6761 (mpt-90) REVERT: G 46 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7557 (mp10) REVERT: G 64 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: G 109 GLU cc_start: 0.4727 (pm20) cc_final: 0.4236 (pm20) REVERT: G 115 LEU cc_start: 0.5406 (OUTLIER) cc_final: 0.4879 (pp) REVERT: G 206 GLN cc_start: 0.5582 (OUTLIER) cc_final: 0.5355 (tm-30) REVERT: h 7 ARG cc_start: 0.6266 (mtp180) cc_final: 0.5876 (ptp-170) REVERT: h 32 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7113 (mtt-85) REVERT: h 112 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6007 (tmt90) REVERT: H 12 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7484 (pt) REVERT: H 28 LYS cc_start: 0.7735 (tmmt) cc_final: 0.7226 (tttp) REVERT: H 35 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6132 (mmt-90) REVERT: H 39 ASN cc_start: 0.7048 (m-40) cc_final: 0.6740 (m-40) REVERT: H 78 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7716 (tp40) REVERT: H 107 GLU cc_start: 0.6524 (tp30) cc_final: 0.6318 (tp30) REVERT: H 128 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6123 (mtp) REVERT: i 38 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7688 (ttmm) REVERT: i 43 MET cc_start: 0.7378 (tpp) cc_final: 0.7137 (mmt) REVERT: i 59 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6467 (tp30) REVERT: i 84 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7037 (tttt) REVERT: i 99 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5388 (ttpp) REVERT: I 32 ARG cc_start: 0.7165 (mmm160) cc_final: 0.6822 (mmm160) REVERT: I 202 ASN cc_start: 0.6741 (m110) cc_final: 0.6527 (m-40) REVERT: I 213 HIS cc_start: 0.4501 (t70) cc_final: 0.3912 (t-170) REVERT: J 33 LEU cc_start: 0.7103 (tp) cc_final: 0.6746 (tp) REVERT: J 34 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7246 (p) REVERT: J 58 ARG cc_start: 0.5029 (tpt90) cc_final: 0.4719 (tpp80) REVERT: J 175 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5507 (pt) REVERT: k 3 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6721 (mtt90) REVERT: k 9 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7083 (mmmt) REVERT: k 60 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.6026 (mp) REVERT: L 155 MET cc_start: 0.7996 (mtp) cc_final: 0.7777 (mtm) REVERT: L 164 GLU cc_start: 0.5710 (mp0) cc_final: 0.5506 (mt-10) REVERT: L 190 ARG cc_start: 0.7394 (ttp-110) cc_final: 0.6931 (ttt90) REVERT: L 195 ARG cc_start: 0.7129 (ttm110) cc_final: 0.6678 (mtm180) REVERT: l 28 ARG cc_start: 0.7280 (mtp180) cc_final: 0.7060 (mtp180) REVERT: M 57 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8043 (pp) REVERT: M 104 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7293 (tpp) REVERT: N 9 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: N 161 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6660 (mpt) REVERT: n 18 ARG cc_start: 0.7180 (mtm-85) cc_final: 0.6769 (mtm110) REVERT: O 49 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7339 (ttm-80) REVERT: O 61 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7557 (ptt-90) REVERT: O 132 THR cc_start: 0.7469 (m) cc_final: 0.7200 (t) REVERT: O 191 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.6081 (mpp-170) REVERT: o 25 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7600 (tp40) REVERT: o 28 LYS cc_start: 0.7474 (tptm) cc_final: 0.6965 (mtmt) REVERT: o 30 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6501 (mtpp) REVERT: o 71 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6630 (tt0) REVERT: o 87 ARG cc_start: 0.8636 (ptp-110) cc_final: 0.8162 (ptm160) REVERT: P 104 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: P 133 LEU cc_start: 0.7942 (tm) cc_final: 0.7647 (tm) REVERT: P 155 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7357 (ttm-80) REVERT: p 10 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7860 (tp) REVERT: p 61 MET cc_start: 0.7559 (mmm) cc_final: 0.7308 (mmm) REVERT: p 78 THR cc_start: 0.8004 (m) cc_final: 0.7793 (m) REVERT: Q 150 ARG cc_start: 0.7995 (mtt-85) cc_final: 0.7626 (mtt180) REVERT: r 35 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7757 (ptp90) REVERT: r 101 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7547 (mttm) REVERT: R 44 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7789 (tp) REVERT: R 52 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7414 (ttp80) REVERT: R 89 MET cc_start: 0.7918 (tpt) cc_final: 0.7595 (tpt) REVERT: R 151 ARG cc_start: 0.6888 (tpt170) cc_final: 0.6398 (tpp80) REVERT: R 154 LEU cc_start: 0.7557 (tm) cc_final: 0.7079 (tt) REVERT: S 132 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7849 (pt) REVERT: T 14 MET cc_start: 0.7537 (ttm) cc_final: 0.6969 (ttm) REVERT: T 87 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7386 (mtpp) REVERT: T 122 LYS cc_start: 0.3226 (mmtp) cc_final: 0.1590 (tppt) REVERT: U 71 THR cc_start: 0.5599 (OUTLIER) cc_final: 0.5185 (t) REVERT: U 109 SER cc_start: 0.7578 (t) cc_final: 0.7294 (t) REVERT: U 116 GLN cc_start: 0.6013 (OUTLIER) cc_final: 0.5685 (mp10) REVERT: W 28 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7657 (t) REVERT: W 47 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5960 (mtt-85) REVERT: X 41 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6481 (mtt-85) REVERT: X 87 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6462 (mpm) REVERT: Y 17 ARG cc_start: 0.7370 (ptp-110) cc_final: 0.7058 (ptp-170) outliers start: 455 outliers final: 254 residues processed: 1159 average time/residue: 2.1317 time to fit residues: 3475.2303 Evaluate side-chains 1139 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 818 time to evaluate : 6.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 88 VAL Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain u residue 67 ASN Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain b residue 31 SER Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 51 LYS Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 63 ARG Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain e residue 32 LYS Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 88 ARG Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 112 ARG Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain i residue 99 LYS Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 82 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain k residue 3 ARG Chi-restraints excluded: chain k residue 9 LYS Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 60 LEU Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 21 ARG Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 179 LYS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 170 LYS Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 25 GLN Chi-restraints excluded: chain o residue 30 LYS Chi-restraints excluded: chain o residue 67 VAL Chi-restraints excluded: chain o residue 71 GLU Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 155 ARG Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 38 THR Chi-restraints excluded: chain p residue 48 LYS Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 35 ARG Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain r residue 120 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 52 ARG Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 116 GLN Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain V residue 108 ASN Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 134 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 77 ILE Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 951 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 562 optimal weight: 5.9990 chunk 720 optimal weight: 30.0000 chunk 558 optimal weight: 20.0000 chunk 830 optimal weight: 20.0000 chunk 551 optimal weight: 6.9990 chunk 983 optimal weight: 20.0000 chunk 615 optimal weight: 20.0000 chunk 599 optimal weight: 20.0000 chunk 453 optimal weight: 9.9990 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 108 ASN ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN D 222 GLN e 102 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN G 159 HIS J 42 GLN J 46 GLN J 168 GLN ** k 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 HIS l 25 GLN N 29 GLN N 37 HIS ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 HIS P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 ASN ** Q 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 HIS S 173 ASN W 50 ASN ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 145005 Z= 0.359 Angle : 0.810 30.091 213974 Z= 0.407 Chirality : 0.046 0.420 26687 Planarity : 0.007 0.091 13041 Dihedral : 24.643 179.798 67368 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.54 % Favored : 93.41 % Rotamer: Outliers : 8.02 % Allowed : 21.18 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.10), residues: 6529 helix: 0.45 (0.11), residues: 2185 sheet: -0.70 (0.16), residues: 921 loop : -1.50 (0.10), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP j 49 HIS 0.021 0.002 HIS R 143 PHE 0.023 0.002 PHE Q 174 TYR 0.036 0.003 TYR D 210 ARG 0.013 0.001 ARG J 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 456 poor density : 846 time to evaluate : 6.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6815 (ptm160) REVERT: A 36 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: A 93 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7520 (mmmm) REVERT: A 125 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7801 (mmtt) REVERT: b 65 MET cc_start: 0.5222 (tmm) cc_final: 0.3806 (mmt) REVERT: B 240 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8172 (mt) REVERT: B 345 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7528 (mt) REVERT: B 354 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6488 (mp10) REVERT: c 18 LEU cc_start: 0.7959 (tp) cc_final: 0.7672 (tp) REVERT: c 38 ILE cc_start: 0.8209 (mt) cc_final: 0.7970 (mt) REVERT: c 40 GLN cc_start: 0.7367 (tp40) cc_final: 0.6832 (mt0) REVERT: c 57 LYS cc_start: 0.7785 (ttpt) cc_final: 0.7314 (tttp) REVERT: c 61 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6632 (mt-10) REVERT: c 78 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7210 (p0) REVERT: C 61 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: C 147 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8352 (t) REVERT: C 230 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7759 (pp) REVERT: d 51 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7428 (mtpm) REVERT: d 54 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.5668 (tmm) REVERT: d 63 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7230 (mtm-85) REVERT: d 67 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7072 (mtt90) REVERT: D 85 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7076 (tptp) REVERT: D 104 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7432 (mt) REVERT: D 210 TYR cc_start: 0.6298 (t80) cc_final: 0.5764 (t80) REVERT: e 128 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.5609 (ttm170) REVERT: E 115 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6475 (pp20) REVERT: E 148 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7263 (mt) REVERT: f 22 ARG cc_start: 0.8570 (mmt180) cc_final: 0.8329 (mmt-90) REVERT: F 32 ILE cc_start: 0.6609 (OUTLIER) cc_final: 0.6252 (mm) REVERT: F 64 ARG cc_start: 0.7811 (tmm-80) cc_final: 0.7428 (ttp-110) REVERT: F 112 GLN cc_start: 0.7867 (pt0) cc_final: 0.7660 (pt0) REVERT: F 132 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7730 (mp) REVERT: F 179 ARG cc_start: 0.6611 (mtt-85) cc_final: 0.6388 (mtt-85) REVERT: F 202 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6800 (mpt-90) REVERT: G 46 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7599 (mp10) REVERT: G 64 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: G 112 GLN cc_start: 0.5058 (OUTLIER) cc_final: 0.3987 (mm-40) REVERT: G 115 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.4915 (pp) REVERT: G 210 GLU cc_start: 0.5219 (OUTLIER) cc_final: 0.4701 (mm-30) REVERT: G 220 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5729 (mm-30) REVERT: h 7 ARG cc_start: 0.6334 (mtp180) cc_final: 0.5940 (ptp-170) REVERT: h 32 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7046 (mtt-85) REVERT: h 112 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6211 (tmt90) REVERT: H 12 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7433 (pt) REVERT: H 28 LYS cc_start: 0.7759 (tmmt) cc_final: 0.7471 (ttpp) REVERT: H 78 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7604 (tp40) REVERT: H 128 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6078 (mtp) REVERT: i 7 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7107 (mtm) REVERT: i 32 ARG cc_start: 0.6993 (mmt180) cc_final: 0.6266 (mtp-110) REVERT: i 38 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7031 (tptp) REVERT: i 59 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6615 (tp30) REVERT: i 84 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6946 (tttt) REVERT: i 99 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5468 (tppp) REVERT: I 32 ARG cc_start: 0.7167 (mmm160) cc_final: 0.6853 (mmm160) REVERT: I 43 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7401 (t) REVERT: I 115 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7214 (mmm) REVERT: I 202 ASN cc_start: 0.6817 (m110) cc_final: 0.6611 (m-40) REVERT: J 115 LEU cc_start: 0.6480 (mt) cc_final: 0.6180 (mp) REVERT: J 175 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5573 (pt) REVERT: L 160 VAL cc_start: 0.6133 (OUTLIER) cc_final: 0.5662 (t) REVERT: L 190 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.6937 (ttt90) REVERT: L 195 ARG cc_start: 0.6936 (ttm110) cc_final: 0.6615 (mtm180) REVERT: l 28 ARG cc_start: 0.7339 (mtp180) cc_final: 0.7122 (mtp180) REVERT: M 57 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7997 (pp) REVERT: M 104 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7768 (mmm) REVERT: m 113 LYS cc_start: 0.7913 (mttp) cc_final: 0.7626 (tttt) REVERT: N 9 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: N 161 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6749 (mpt) REVERT: n 14 LYS cc_start: 0.4710 (mmtt) cc_final: 0.4484 (mmtt) REVERT: n 18 ARG cc_start: 0.7170 (mtm-85) cc_final: 0.6746 (mtm110) REVERT: O 49 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7278 (ttm-80) REVERT: O 61 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7556 (ptt-90) REVERT: O 132 THR cc_start: 0.7469 (m) cc_final: 0.7190 (t) REVERT: O 191 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6145 (mpp-170) REVERT: o 25 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7691 (tp40) REVERT: o 28 LYS cc_start: 0.7432 (tptm) cc_final: 0.6996 (mtmt) REVERT: o 71 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6620 (tt0) REVERT: o 87 ARG cc_start: 0.8632 (ptp-110) cc_final: 0.8177 (ptm160) REVERT: P 104 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7194 (tt0) REVERT: P 155 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7393 (ttm-80) REVERT: p 10 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7998 (tp) REVERT: p 61 MET cc_start: 0.7591 (mmm) cc_final: 0.7345 (mmm) REVERT: p 78 THR cc_start: 0.7994 (m) cc_final: 0.7783 (m) REVERT: p 87 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7100 (tttt) REVERT: Q 14 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6338 (pmm-80) REVERT: Q 150 ARG cc_start: 0.7989 (mtt-85) cc_final: 0.7631 (mmt180) REVERT: r 35 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7894 (ptp90) REVERT: r 71 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5018 (mpt180) REVERT: r 101 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7572 (mttm) REVERT: R 44 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7778 (tp) REVERT: R 89 MET cc_start: 0.7931 (tpt) cc_final: 0.7582 (tpt) REVERT: R 151 ARG cc_start: 0.6999 (tpt170) cc_final: 0.6573 (tpp80) REVERT: R 154 LEU cc_start: 0.7482 (tm) cc_final: 0.7093 (tt) REVERT: R 158 GLN cc_start: 0.5240 (tm-30) cc_final: 0.4856 (tt0) REVERT: S 96 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: S 132 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7959 (pt) REVERT: T 14 MET cc_start: 0.7570 (ttm) cc_final: 0.7009 (ttm) REVERT: T 31 MET cc_start: 0.7632 (mtp) cc_final: 0.7242 (mtm) REVERT: T 41 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6798 (p0) REVERT: T 87 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7354 (mtpp) REVERT: T 122 LYS cc_start: 0.4085 (mmtp) cc_final: 0.1988 (tppt) REVERT: U 109 SER cc_start: 0.7580 (t) cc_final: 0.7300 (t) REVERT: U 116 GLN cc_start: 0.5932 (OUTLIER) cc_final: 0.5555 (mp10) REVERT: W 1 MET cc_start: 0.2360 (tpt) cc_final: 0.1183 (mmm) REVERT: W 25 ASP cc_start: 0.7670 (p0) cc_final: 0.7415 (p0) REVERT: W 47 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6019 (mtt-85) REVERT: W 57 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7230 (ttm-80) REVERT: X 40 ILE cc_start: 0.6313 (pt) cc_final: 0.6068 (pt) REVERT: X 41 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6472 (mtt-85) REVERT: X 87 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6488 (mpm) REVERT: X 133 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6556 (mm-30) REVERT: X 145 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6626 (t70) REVERT: X 151 ASN cc_start: 0.6602 (m110) cc_final: 0.6305 (m-40) REVERT: Y 17 ARG cc_start: 0.7448 (ptp-110) cc_final: 0.7142 (ptp-170) REVERT: Z 106 LEU cc_start: 0.6724 (mm) cc_final: 0.6422 (mt) REVERT: a 105 ARG cc_start: 0.5715 (OUTLIER) cc_final: 0.4220 (ttt180) REVERT: a 114 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8225 (tttt) outliers start: 456 outliers final: 272 residues processed: 1153 average time/residue: 2.1701 time to fit residues: 3534.6158 Evaluate side-chains 1164 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 343 poor density : 821 time to evaluate : 6.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 88 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain u residue 67 ASN Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain b residue 31 SER Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 51 LYS Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 63 ARG Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain e residue 53 ILE Chi-restraints excluded: chain e residue 57 ASN Chi-restraints excluded: chain e residue 91 CYS Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 88 ARG Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 64 GLN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 112 ARG Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain i residue 7 MET Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain i residue 99 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 82 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 21 ARG Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 152 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 179 LYS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 170 LYS Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 25 GLN Chi-restraints excluded: chain o residue 67 VAL Chi-restraints excluded: chain o residue 71 GLU Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 155 ARG Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 38 THR Chi-restraints excluded: chain p residue 48 LYS Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain Q residue 14 ARG Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 35 ARG Chi-restraints excluded: chain r residue 71 ARG Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain r residue 120 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 91 GLU Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 96 LEU Chi-restraints excluded: chain U residue 116 GLN Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 45 ILE Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 108 ASN Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 134 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 43 SER Chi-restraints excluded: chain X residue 77 ILE Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 145 ASP Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 50 ARG Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 109 LYS Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 105 ARG Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 140 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 608 optimal weight: 20.0000 chunk 392 optimal weight: 10.0000 chunk 587 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 193 optimal weight: 0.1980 chunk 190 optimal weight: 7.9990 chunk 625 optimal weight: 20.0000 chunk 669 optimal weight: 30.0000 chunk 486 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 772 optimal weight: 30.0000 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN e 102 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN G 64 GLN G 159 HIS I 166 HIS ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 HIS l 25 GLN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN N 37 HIS N 87 HIS o 90 HIS P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 145005 Z= 0.264 Angle : 0.709 28.995 213974 Z= 0.359 Chirality : 0.041 0.333 26687 Planarity : 0.006 0.092 13041 Dihedral : 24.524 179.953 67368 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.79 % Favored : 94.20 % Rotamer: Outliers : 7.21 % Allowed : 22.29 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.10), residues: 6529 helix: 0.72 (0.11), residues: 2191 sheet: -0.62 (0.16), residues: 924 loop : -1.42 (0.10), residues: 3414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP j 49 HIS 0.011 0.001 HIS R 143 PHE 0.018 0.002 PHE D 287 TYR 0.026 0.002 TYR D 44 ARG 0.010 0.001 ARG H 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 410 poor density : 843 time to evaluate : 6.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6720 (ptm160) REVERT: A 36 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: A 125 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7796 (mmtt) REVERT: b 65 MET cc_start: 0.5151 (tmm) cc_final: 0.3702 (mmt) REVERT: B 24 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7724 (ptp-110) REVERT: B 240 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8083 (mt) REVERT: B 345 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7566 (mt) REVERT: B 354 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6404 (mp10) REVERT: B 357 ARG cc_start: 0.7012 (mtt90) cc_final: 0.6784 (mtp85) REVERT: c 18 LEU cc_start: 0.7980 (tp) cc_final: 0.7623 (tp) REVERT: c 38 ILE cc_start: 0.8152 (mt) cc_final: 0.7862 (mt) REVERT: c 40 GLN cc_start: 0.7397 (tp40) cc_final: 0.6819 (mt0) REVERT: c 57 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7302 (tttp) REVERT: c 61 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6605 (mt-10) REVERT: c 78 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7100 (p0) REVERT: C 61 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: C 147 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8337 (t) REVERT: C 230 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7744 (pp) REVERT: d 51 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7365 (mtpm) REVERT: d 54 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5627 (tmm) REVERT: d 63 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7225 (mtm-85) REVERT: d 67 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7012 (mtt90) REVERT: D 85 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7002 (tptp) REVERT: e 121 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7431 (ttt180) REVERT: e 128 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5582 (ttm170) REVERT: E 115 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6512 (pp20) REVERT: E 216 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.5948 (mttt) REVERT: F 64 ARG cc_start: 0.7740 (tmm-80) cc_final: 0.7386 (ttp-110) REVERT: F 112 GLN cc_start: 0.7818 (pt0) cc_final: 0.7362 (mt0) REVERT: F 132 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7702 (mp) REVERT: F 179 ARG cc_start: 0.6626 (mtt-85) cc_final: 0.6354 (mtt-85) REVERT: F 202 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6755 (mpt-90) REVERT: G 46 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7536 (mp10) REVERT: G 112 GLN cc_start: 0.4999 (tm-30) cc_final: 0.4050 (mm-40) REVERT: G 115 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.4955 (pp) REVERT: G 210 GLU cc_start: 0.4893 (OUTLIER) cc_final: 0.4360 (mm-30) REVERT: G 220 GLU cc_start: 0.5942 (mm-30) cc_final: 0.5529 (mm-30) REVERT: h 7 ARG cc_start: 0.6288 (mtp180) cc_final: 0.5902 (ptp-170) REVERT: h 15 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.5427 (mm-30) REVERT: h 32 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7085 (mtt-85) REVERT: h 112 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6193 (tmt90) REVERT: H 12 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7407 (pt) REVERT: H 28 LYS cc_start: 0.7719 (tmmt) cc_final: 0.7186 (tttp) REVERT: H 35 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6128 (mmt-90) REVERT: H 78 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7730 (tp40) REVERT: H 128 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6122 (mtp) REVERT: i 32 ARG cc_start: 0.6970 (mmt180) cc_final: 0.6256 (mtp-110) REVERT: i 38 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7655 (ttmm) REVERT: i 43 MET cc_start: 0.7424 (tpp) cc_final: 0.7192 (mmt) REVERT: i 59 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6379 (tp30) REVERT: i 84 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7000 (tttt) REVERT: i 99 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5546 (ptpt) REVERT: I 32 ARG cc_start: 0.7172 (mmm160) cc_final: 0.6875 (mmm160) REVERT: L 160 VAL cc_start: 0.6052 (OUTLIER) cc_final: 0.5603 (t) REVERT: L 190 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.6943 (ttt90) REVERT: l 28 ARG cc_start: 0.7338 (mtp180) cc_final: 0.7135 (mtp180) REVERT: M 4 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6879 (mtt180) REVERT: M 57 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7939 (pp) REVERT: M 104 MET cc_start: 0.8072 (mmp) cc_final: 0.7805 (mtp) REVERT: N 9 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: N 161 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6733 (mpt) REVERT: n 14 LYS cc_start: 0.4722 (mmtt) cc_final: 0.4327 (mmtt) REVERT: n 18 ARG cc_start: 0.7175 (mtm-85) cc_final: 0.6763 (mtm110) REVERT: n 21 ARG cc_start: 0.7211 (ttt-90) cc_final: 0.5306 (tpt170) REVERT: n 23 ARG cc_start: 0.6355 (mtp85) cc_final: 0.6009 (ttt90) REVERT: O 49 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7362 (ttm-80) REVERT: O 61 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7559 (ptt-90) REVERT: O 132 THR cc_start: 0.7437 (m) cc_final: 0.7222 (t) REVERT: O 191 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6097 (mpp-170) REVERT: o 25 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7642 (tp40) REVERT: o 87 ARG cc_start: 0.8635 (ptp-110) cc_final: 0.8169 (ptm160) REVERT: P 104 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: P 155 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7371 (ttm-80) REVERT: p 10 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7843 (tp) REVERT: p 61 MET cc_start: 0.7561 (mmm) cc_final: 0.7335 (mmm) REVERT: p 78 THR cc_start: 0.7939 (m) cc_final: 0.7725 (m) REVERT: Q 14 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6264 (pmm-80) REVERT: Q 150 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7605 (mmt180) REVERT: r 35 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7738 (ptp90) REVERT: r 71 ARG cc_start: 0.6091 (ptt180) cc_final: 0.5089 (mpt180) REVERT: r 101 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7544 (mttm) REVERT: R 44 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7813 (tp) REVERT: R 89 MET cc_start: 0.7916 (tpt) cc_final: 0.7596 (tpt) REVERT: R 106 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7547 (mp) REVERT: R 151 ARG cc_start: 0.6977 (tpt170) cc_final: 0.6487 (tpp80) REVERT: R 154 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7191 (tt) REVERT: R 158 GLN cc_start: 0.5054 (tm-30) cc_final: 0.4715 (tt0) REVERT: S 54 MET cc_start: 0.6545 (mtp) cc_final: 0.6306 (ptm) REVERT: S 132 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7895 (pt) REVERT: T 14 MET cc_start: 0.7525 (ttm) cc_final: 0.6953 (ttm) REVERT: T 87 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7255 (mtpp) REVERT: T 150 LEU cc_start: 0.8171 (mt) cc_final: 0.7924 (tp) REVERT: U 109 SER cc_start: 0.7525 (t) cc_final: 0.7251 (t) REVERT: U 116 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5723 (mp10) REVERT: W 1 MET cc_start: 0.2397 (tpt) cc_final: 0.1435 (mmm) REVERT: W 28 VAL cc_start: 0.7885 (OUTLIER) cc_final: 0.7637 (t) REVERT: W 47 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.5948 (mtt-85) REVERT: X 40 ILE cc_start: 0.6143 (pt) cc_final: 0.5891 (pt) REVERT: X 41 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6488 (mtt-85) REVERT: X 87 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6497 (mpm) REVERT: X 133 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6555 (mm-30) REVERT: X 151 ASN cc_start: 0.6578 (m110) cc_final: 0.6264 (m-40) REVERT: Y 17 ARG cc_start: 0.7337 (ptp-110) cc_final: 0.7054 (ptp-170) REVERT: Z 106 LEU cc_start: 0.6927 (mm) cc_final: 0.6615 (mt) REVERT: a 105 ARG cc_start: 0.5685 (OUTLIER) cc_final: 0.4266 (ttt180) REVERT: a 114 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8243 (tttt) outliers start: 410 outliers final: 255 residues processed: 1113 average time/residue: 2.1797 time to fit residues: 3410.0085 Evaluate side-chains 1130 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 813 time to evaluate : 6.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 88 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain b residue 31 SER Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 51 LYS Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 63 ARG Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 88 ARG Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 15 GLU Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 112 ARG Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 99 LYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 207 ASP Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 82 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 21 ARG Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 179 LYS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 170 LYS Chi-restraints excluded: chain O residue 184 ASN Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 25 GLN Chi-restraints excluded: chain o residue 67 VAL Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 155 ARG Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 38 THR Chi-restraints excluded: chain p residue 48 LYS Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 14 ARG Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain r residue 8 MET Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 35 ARG Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain r residue 120 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 91 GLU Chi-restraints excluded: chain R residue 99 MET Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 116 GLN Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 91 LYS Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 108 ASN Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 134 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 43 SER Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 105 ARG Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 140 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 894 optimal weight: 20.0000 chunk 941 optimal weight: 20.0000 chunk 859 optimal weight: 20.0000 chunk 916 optimal weight: 20.0000 chunk 551 optimal weight: 3.9990 chunk 399 optimal weight: 1.9990 chunk 719 optimal weight: 40.0000 chunk 281 optimal weight: 9.9990 chunk 827 optimal weight: 20.0000 chunk 866 optimal weight: 20.0000 chunk 912 optimal weight: 20.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN e 102 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN G 64 GLN G 159 HIS G 195 HIS J 42 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** k 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 HIS l 25 GLN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN N 37 HIS ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 184 ASN o 19 GLN o 90 HIS P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 ASN ** Q 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 ASN ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 145005 Z= 0.447 Angle : 0.899 34.336 213974 Z= 0.447 Chirality : 0.050 0.452 26687 Planarity : 0.007 0.092 13041 Dihedral : 24.736 179.920 67368 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.03 % Favored : 92.91 % Rotamer: Outliers : 7.14 % Allowed : 22.45 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.10), residues: 6529 helix: 0.31 (0.11), residues: 2171 sheet: -0.86 (0.16), residues: 928 loop : -1.56 (0.10), residues: 3430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP j 49 HIS 0.013 0.002 HIS R 143 PHE 0.026 0.003 PHE Q 174 TYR 0.027 0.003 TYR Q 32 ARG 0.011 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 823 time to evaluate : 6.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6813 (ptm160) REVERT: A 36 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: A 125 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7720 (mmtt) REVERT: b 65 MET cc_start: 0.5284 (tmm) cc_final: 0.3880 (mmt) REVERT: B 240 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8194 (mt) REVERT: B 345 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7558 (mt) REVERT: B 354 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: c 18 LEU cc_start: 0.7873 (tp) cc_final: 0.7637 (tp) REVERT: c 40 GLN cc_start: 0.7313 (tp40) cc_final: 0.6809 (mt0) REVERT: c 57 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7185 (tttp) REVERT: c 61 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6634 (mt-10) REVERT: c 78 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7298 (p0) REVERT: c 103 ASP cc_start: 0.6226 (p0) cc_final: 0.6009 (p0) REVERT: C 147 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8351 (t) REVERT: C 230 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7795 (pp) REVERT: C 281 MET cc_start: 0.7793 (mmp) cc_final: 0.7430 (mpm) REVERT: d 51 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7459 (mtpm) REVERT: d 54 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.5681 (tmm) REVERT: d 63 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7236 (mtm-85) REVERT: d 67 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7082 (mtt90) REVERT: d 91 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7786 (mppt) REVERT: D 85 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7070 (tptp) REVERT: D 133 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5514 (pp20) REVERT: e 128 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.5700 (ttm170) REVERT: E 115 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6495 (pp20) REVERT: E 216 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6208 (mttt) REVERT: f 22 ARG cc_start: 0.8575 (mmt180) cc_final: 0.8352 (mmt-90) REVERT: F 64 ARG cc_start: 0.7851 (tmm-80) cc_final: 0.7441 (ttp-110) REVERT: F 132 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7799 (mp) REVERT: F 179 ARG cc_start: 0.6535 (mtt-85) cc_final: 0.6294 (mtt-85) REVERT: F 202 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6603 (mpt-90) REVERT: G 46 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7596 (mp10) REVERT: G 112 GLN cc_start: 0.5079 (tm-30) cc_final: 0.4039 (mm-40) REVERT: G 115 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5301 (pp) REVERT: G 210 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.4740 (mm-30) REVERT: G 220 GLU cc_start: 0.6087 (mm-30) cc_final: 0.5673 (mm-30) REVERT: h 7 ARG cc_start: 0.6377 (mtp180) cc_final: 0.6013 (ptp-170) REVERT: h 15 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.5435 (mm-30) REVERT: h 32 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7130 (mtt-85) REVERT: H 12 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7495 (pt) REVERT: H 28 LYS cc_start: 0.7747 (tmmt) cc_final: 0.7495 (ttpp) REVERT: H 78 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7640 (tp40) REVERT: H 96 TYR cc_start: 0.7544 (p90) cc_final: 0.7276 (p90) REVERT: H 128 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6040 (mtp) REVERT: i 7 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7274 (mtm) REVERT: i 38 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7081 (tptp) REVERT: i 84 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6988 (tttt) REVERT: I 43 VAL cc_start: 0.7746 (OUTLIER) cc_final: 0.7442 (t) REVERT: I 115 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7242 (mmm) REVERT: J 115 LEU cc_start: 0.6463 (mt) cc_final: 0.6159 (mp) REVERT: L 190 ARG cc_start: 0.7292 (ttp-110) cc_final: 0.6901 (ttt90) REVERT: l 28 ARG cc_start: 0.7366 (mtp180) cc_final: 0.7133 (mtp180) REVERT: M 4 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6746 (mtt180) REVERT: M 57 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8019 (pp) REVERT: m 113 LYS cc_start: 0.7935 (mttp) cc_final: 0.7639 (tttt) REVERT: N 9 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: N 161 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6747 (mpt) REVERT: n 14 LYS cc_start: 0.4758 (mmtt) cc_final: 0.4403 (mmtt) REVERT: n 16 LYS cc_start: 0.7788 (tptt) cc_final: 0.7117 (ttmm) REVERT: n 18 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6837 (mtm110) REVERT: n 23 ARG cc_start: 0.6532 (mtp85) cc_final: 0.6093 (ttt90) REVERT: O 49 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7365 (ttm-80) REVERT: O 61 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7556 (ptt-90) REVERT: O 132 THR cc_start: 0.7476 (m) cc_final: 0.7183 (t) REVERT: O 180 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6171 (tm-30) REVERT: O 191 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6120 (mpp-170) REVERT: o 13 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6266 (mtpt) REVERT: o 25 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7816 (tp40) REVERT: o 87 ARG cc_start: 0.8613 (ptp-110) cc_final: 0.8163 (ptm160) REVERT: P 104 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: p 10 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8025 (tp) REVERT: p 61 MET cc_start: 0.7581 (mmm) cc_final: 0.7322 (mmm) REVERT: p 78 THR cc_start: 0.8000 (m) cc_final: 0.7791 (m) REVERT: p 87 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7137 (tttt) REVERT: Q 150 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7645 (mmt180) REVERT: r 101 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7609 (mtpt) REVERT: R 44 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7872 (tp) REVERT: R 52 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7413 (ttp80) REVERT: R 89 MET cc_start: 0.7966 (tpt) cc_final: 0.7618 (tpt) REVERT: R 151 ARG cc_start: 0.7059 (tpt170) cc_final: 0.6534 (tpp80) REVERT: R 154 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7104 (tt) REVERT: S 132 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7966 (pt) REVERT: T 14 MET cc_start: 0.7630 (ttm) cc_final: 0.7082 (ttm) REVERT: T 41 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6752 (p0) REVERT: U 109 SER cc_start: 0.7598 (t) cc_final: 0.7321 (t) REVERT: U 116 GLN cc_start: 0.5952 (OUTLIER) cc_final: 0.5571 (mp10) REVERT: W 1 MET cc_start: 0.2462 (tpt) cc_final: 0.1393 (mmm) REVERT: W 47 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6198 (mtt-85) REVERT: X 40 ILE cc_start: 0.6231 (pt) cc_final: 0.6004 (pt) REVERT: X 41 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6464 (mtt-85) REVERT: X 87 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.6514 (mpm) REVERT: X 133 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6609 (mm-30) REVERT: X 151 ASN cc_start: 0.6601 (m110) cc_final: 0.6332 (m-40) REVERT: Y 17 ARG cc_start: 0.7598 (ptp-110) cc_final: 0.7334 (ptp-170) REVERT: a 105 ARG cc_start: 0.5745 (OUTLIER) cc_final: 0.4271 (ttt180) outliers start: 406 outliers final: 287 residues processed: 1088 average time/residue: 2.1384 time to fit residues: 3283.4563 Evaluate side-chains 1150 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 805 time to evaluate : 6.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 88 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain u residue 64 MET Chi-restraints excluded: chain u residue 67 ASN Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain b residue 31 SER Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 51 LYS Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 63 ARG Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 91 LYS Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 88 ARG Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 15 GLU Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 112 ARG Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain i residue 7 MET Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 59 GLU Chi-restraints excluded: chain i residue 61 LEU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 94 LEU Chi-restraints excluded: chain i residue 99 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 82 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 21 ARG Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 179 LYS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 180 GLN Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 25 GLN Chi-restraints excluded: chain o residue 67 VAL Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 38 THR Chi-restraints excluded: chain p residue 48 LYS Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain r residue 120 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 52 ARG Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 96 LEU Chi-restraints excluded: chain U residue 116 GLN Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain V residue 108 ASN Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 134 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 43 SER Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 50 ARG Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 68 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 105 ARG Chi-restraints excluded: chain a residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 601 optimal weight: 10.0000 chunk 968 optimal weight: 8.9990 chunk 591 optimal weight: 8.9990 chunk 459 optimal weight: 8.9990 chunk 673 optimal weight: 9.9990 chunk 1016 optimal weight: 6.9990 chunk 935 optimal weight: 10.0000 chunk 809 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 625 optimal weight: 20.0000 chunk 496 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 50 ASN ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN e 102 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN G 64 GLN G 159 HIS J 42 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 HIS l 25 GLN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 87 GLN N 29 GLN N 37 HIS ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 HIS P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 145005 Z= 0.296 Angle : 0.747 30.877 213974 Z= 0.377 Chirality : 0.043 0.351 26687 Planarity : 0.006 0.092 13041 Dihedral : 24.599 179.934 67368 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 6.49 % Allowed : 23.33 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.10), residues: 6529 helix: 0.60 (0.11), residues: 2184 sheet: -0.69 (0.16), residues: 933 loop : -1.50 (0.10), residues: 3412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP j 49 HIS 0.012 0.002 HIS R 143 PHE 0.021 0.002 PHE D 287 TYR 0.027 0.002 TYR D 44 ARG 0.010 0.001 ARG J 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 842 time to evaluate : 6.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6801 (ptm160) REVERT: A 36 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: A 125 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7743 (mmtt) REVERT: b 65 MET cc_start: 0.4985 (tmm) cc_final: 0.3726 (mmt) REVERT: B 24 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7630 (ptp-110) REVERT: B 240 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8121 (mt) REVERT: B 345 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7526 (mt) REVERT: B 354 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6456 (mp10) REVERT: c 18 LEU cc_start: 0.7894 (tp) cc_final: 0.7636 (tp) REVERT: c 40 GLN cc_start: 0.7423 (tp40) cc_final: 0.6864 (mt0) REVERT: c 57 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7314 (tttp) REVERT: c 61 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6612 (mt-10) REVERT: c 78 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7153 (p0) REVERT: c 103 ASP cc_start: 0.6126 (p0) cc_final: 0.5857 (p0) REVERT: C 61 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: C 147 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8349 (t) REVERT: C 230 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7769 (pp) REVERT: C 281 MET cc_start: 0.7775 (mmp) cc_final: 0.7443 (mpm) REVERT: d 54 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.5585 (tmm) REVERT: d 63 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7240 (mtm-85) REVERT: d 67 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7078 (mtt90) REVERT: D 85 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6993 (tptp) REVERT: e 121 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7442 (ttt180) REVERT: e 128 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5636 (ttm170) REVERT: E 115 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6508 (pp20) REVERT: E 216 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.5932 (mttt) REVERT: F 64 ARG cc_start: 0.7799 (tmm-80) cc_final: 0.7428 (ttp-110) REVERT: F 132 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7708 (mp) REVERT: F 202 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6787 (mpt-90) REVERT: G 46 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7570 (mp10) REVERT: G 112 GLN cc_start: 0.4972 (tm-30) cc_final: 0.4134 (mm-40) REVERT: G 115 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5314 (pp) REVERT: G 210 GLU cc_start: 0.5457 (OUTLIER) cc_final: 0.4813 (mm-30) REVERT: G 220 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5547 (mm-30) REVERT: h 7 ARG cc_start: 0.6337 (mtp180) cc_final: 0.5950 (ptp-170) REVERT: h 15 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5495 (mm-30) REVERT: h 32 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7123 (mtt-85) REVERT: h 112 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6214 (tmt90) REVERT: H 12 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7401 (pt) REVERT: H 28 LYS cc_start: 0.7745 (tmmt) cc_final: 0.7478 (ttpp) REVERT: H 78 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7658 (tp40) REVERT: H 128 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6159 (mtp) REVERT: i 32 ARG cc_start: 0.6968 (mmt180) cc_final: 0.6254 (mtp-110) REVERT: i 38 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7682 (ttmm) REVERT: i 43 MET cc_start: 0.7477 (tpp) cc_final: 0.7257 (mmt) REVERT: i 84 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7015 (tttt) REVERT: i 99 LYS cc_start: 0.5984 (OUTLIER) cc_final: 0.5641 (ptpt) REVERT: I 43 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7375 (t) REVERT: I 115 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7201 (mmm) REVERT: I 213 HIS cc_start: 0.4583 (t70) cc_final: 0.4208 (t-170) REVERT: J 58 ARG cc_start: 0.5256 (tpt90) cc_final: 0.5043 (tpp80) REVERT: J 115 LEU cc_start: 0.6497 (mt) cc_final: 0.6209 (mp) REVERT: k 3 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6868 (mtt90) REVERT: L 160 VAL cc_start: 0.6168 (OUTLIER) cc_final: 0.5771 (t) REVERT: L 190 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.6974 (ttt90) REVERT: l 28 ARG cc_start: 0.7354 (mtp180) cc_final: 0.7124 (mtp180) REVERT: M 4 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6755 (mtt180) REVERT: M 57 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7976 (pp) REVERT: N 9 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: N 161 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6730 (mpt) REVERT: n 16 LYS cc_start: 0.7844 (tptt) cc_final: 0.7192 (ttmm) REVERT: n 18 ARG cc_start: 0.7151 (mtm-85) cc_final: 0.6723 (mtm110) REVERT: n 21 ARG cc_start: 0.7267 (ttt-90) cc_final: 0.5360 (tpt170) REVERT: n 23 ARG cc_start: 0.6500 (mtp85) cc_final: 0.6267 (ttt90) REVERT: O 49 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7354 (ttm-80) REVERT: O 61 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7571 (ptt-90) REVERT: O 132 THR cc_start: 0.7438 (m) cc_final: 0.7222 (t) REVERT: O 180 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6107 (tm-30) REVERT: O 191 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6059 (mpp-170) REVERT: o 87 ARG cc_start: 0.8632 (ptp-110) cc_final: 0.8165 (ptm160) REVERT: P 104 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: P 133 LEU cc_start: 0.7929 (tm) cc_final: 0.7687 (tm) REVERT: p 10 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7852 (tp) REVERT: p 61 MET cc_start: 0.7562 (mmm) cc_final: 0.7346 (mmm) REVERT: p 78 THR cc_start: 0.7936 (m) cc_final: 0.7724 (m) REVERT: Q 14 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6311 (pmm-80) REVERT: Q 150 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7604 (mmt180) REVERT: r 71 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.4944 (mpt180) REVERT: r 101 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7518 (mttt) REVERT: R 44 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7899 (tp) REVERT: R 52 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7440 (ttp80) REVERT: R 89 MET cc_start: 0.7925 (tpt) cc_final: 0.7577 (tpt) REVERT: R 151 ARG cc_start: 0.7038 (tpt170) cc_final: 0.6530 (tpp80) REVERT: R 154 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7219 (tt) REVERT: R 158 GLN cc_start: 0.5153 (tm-30) cc_final: 0.4742 (tt0) REVERT: S 132 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7905 (pt) REVERT: T 14 MET cc_start: 0.7516 (ttm) cc_final: 0.6976 (ttm) REVERT: T 41 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6733 (p0) REVERT: T 87 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7253 (mtpp) REVERT: T 150 LEU cc_start: 0.8213 (mt) cc_final: 0.7931 (tp) REVERT: U 109 SER cc_start: 0.7550 (t) cc_final: 0.7275 (t) REVERT: U 116 GLN cc_start: 0.5934 (OUTLIER) cc_final: 0.5603 (mp10) REVERT: W 1 MET cc_start: 0.2266 (tpt) cc_final: 0.1286 (mmm) REVERT: W 28 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7659 (t) REVERT: W 47 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6021 (mtt-85) REVERT: W 57 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7188 (ttm-80) REVERT: X 40 ILE cc_start: 0.6075 (pt) cc_final: 0.5853 (pt) REVERT: X 41 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6471 (mtt-85) REVERT: X 87 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6506 (mpm) REVERT: X 133 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6538 (mm-30) REVERT: X 151 ASN cc_start: 0.6575 (m110) cc_final: 0.6306 (m-40) REVERT: Y 17 ARG cc_start: 0.7419 (ptp-110) cc_final: 0.7149 (ptp-170) REVERT: Y 126 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6440 (mtp85) REVERT: Z 30 ASP cc_start: 0.7437 (p0) cc_final: 0.7189 (p0) outliers start: 369 outliers final: 266 residues processed: 1086 average time/residue: 2.1467 time to fit residues: 3280.7113 Evaluate side-chains 1152 residues out of total 5694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 825 time to evaluate : 6.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 88 VAL Chi-restraints excluded: chain t residue 128 ILE Chi-restraints excluded: chain u residue 55 ASN Chi-restraints excluded: chain u residue 67 ASN Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain b residue 31 SER Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain c residue 46 VAL Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain d residue 26 THR Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 63 ARG Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 128 ARG Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 202 ARG Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 88 ARG Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain h residue 3 LYS Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain h residue 14 LYS Chi-restraints excluded: chain h residue 15 GLU Chi-restraints excluded: chain h residue 18 LEU Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 32 ARG Chi-restraints excluded: chain h residue 112 ARG Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 78 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 128 MET Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 172 ILE Chi-restraints excluded: chain i residue 19 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain i residue 84 LYS Chi-restraints excluded: chain i residue 93 VAL Chi-restraints excluded: chain i residue 99 LYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain j residue 6 SER Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 82 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 75 ARG Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain k residue 3 ARG Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 146 LEU Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 21 ARG Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain N residue 147 ASP Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 166 SER Chi-restraints excluded: chain N residue 179 LYS Chi-restraints excluded: chain O residue 49 ARG Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 180 GLN Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain O residue 195 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 25 GLN Chi-restraints excluded: chain o residue 67 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 38 THR Chi-restraints excluded: chain p residue 48 LYS Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 70 THR Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 14 ARG Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 71 ARG Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain r residue 120 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 12 SER Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 52 ARG Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 144 LYS Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 168 THR Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 LYS Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain T residue 63 ARG Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain U residue 116 GLN Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 99 GLU Chi-restraints excluded: chain V residue 108 ASN Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 134 SER Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ASN Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain X residue 41 ARG Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 43 SER Chi-restraints excluded: chain X residue 87 MET Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 126 THR Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 149 VAL Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 45 ARG Chi-restraints excluded: chain Y residue 50 ARG Chi-restraints excluded: chain Y residue 82 ILE Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 126 ARG Chi-restraints excluded: chain Z residue 14 LEU Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 642 optimal weight: 30.0000 chunk 861 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 746 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 810 optimal weight: 20.0000 chunk 339 optimal weight: 9.9990 chunk 832 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 50 ASN ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN e 102 ASN ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 223 HIS ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN G 64 GLN J 42 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 HIS l 25 GLN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 GLN N 29 GLN N 37 HIS ** N 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 HIS P 50 ASN ** P 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 127 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120500 restraints weight = 177598.264| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.30 r_work: 0.3105 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 145005 Z= 0.461 Angle : 0.923 35.317 213974 Z= 0.457 Chirality : 0.051 0.465 26687 Planarity : 0.008 0.093 13041 Dihedral : 24.773 179.924 67368 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 6.98 % Allowed : 22.96 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.10), residues: 6529 helix: 0.24 (0.11), residues: 2168 sheet: -0.87 (0.16), residues: 927 loop : -1.60 (0.10), residues: 3434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 209 HIS 0.013 0.002 HIS R 143 PHE 0.025 0.003 PHE Q 174 TYR 0.036 0.003 TYR B 49 ARG 0.011 0.001 ARG J 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47923.94 seconds wall clock time: 828 minutes 57.44 seconds (49737.44 seconds total)