Starting phenix.real_space_refine on Sat Apr 13 03:27:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/04_2024/7m4z_23671_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/04_2024/7m4z_23671.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/04_2024/7m4z_23671_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/04_2024/7m4z_23671_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/04_2024/7m4z_23671_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/04_2024/7m4z_23671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/04_2024/7m4z_23671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/04_2024/7m4z_23671_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4z_23671/04_2024/7m4z_23671_updated.pdb" } resolution = 2.92 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= 0.006 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4372 5.49 5 Mg 187 5.21 5 S 142 5.16 5 C 69334 2.51 5 N 25630 2.21 5 O 38504 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 9": "OE1" <-> "OE2" Residue "2 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 37": "OD1" <-> "OD2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "K PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "N PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "O ASP 94": "OD1" <-> "OD2" Residue "P ASP 102": "OD1" <-> "OD2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 87": "OD1" <-> "OD2" Residue "V ASP 64": "OD1" <-> "OD2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "Y TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c ASP 107": "OD1" <-> "OD2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "d GLU 97": "OE1" <-> "OE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "g ASP 15": "OD1" <-> "OD2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 35": "OD1" <-> "OD2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 14": "OE1" <-> "OE2" Residue "n TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 92": "OD1" <-> "OD2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 38": "OD1" <-> "OD2" Residue "p ASP 47": "OD1" <-> "OD2" Residue "r TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 59": "OD1" <-> "OD2" Residue "v ASP 55": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 138172 Number of models: 1 Model: "" Number of chains: 70 Chain: "0" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 58566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2730, 58566 Classifications: {'RNA': 2730} Modifications used: {'rna2p': 3, 'rna2p_pur': 247, 'rna2p_pyr': 145, 'rna3p': 12, 'rna3p_pur': 1313, 'rna3p_pyr': 1010} Link IDs: {'rna2p': 394, 'rna3p': 2335} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 50} Link IDs: {'rna2p': 9, 'rna3p': 105} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1566 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 204} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1516 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1117 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "T" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 585 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Y" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "a" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 112, 'rna2p_pyr': 85, 'rna3p': 8, 'rna3p_pur': 751, 'rna3p_pyr': 571} Link IDs: {'rna2p': 197, 'rna3p': 1330} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1188 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "v" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 824 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 215 Unusual residues: {' MG': 135, 'YQM': 2} Classifications: {'undetermined': 137} Link IDs: {None: 136} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Unusual residues: {' MG': 48} Classifications: {'undetermined': 48} Link IDs: {None: 47} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 179 Classifications: {'water': 179} Link IDs: {None: 178} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1364 SG CYS 3 11 181.763 113.095 137.277 1.00 27.52 S ATOM 1380 SG CYS 3 14 180.673 114.656 140.592 1.00 26.86 S ATOM 1485 SG CYS 3 27 182.092 116.821 137.799 1.00 27.50 S Time building chain proxies: 52.77, per 1000 atoms: 0.38 Number of scatterers: 138172 At special positions: 0 Unit cell: (230.656, 245.072, 275.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 142 16.00 P 4372 15.00 Mg 187 11.99 F 2 9.00 O 38504 8.00 N 25630 7.00 C 69334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 53.34 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " Number of angles added : 3 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10316 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 171 helices and 71 sheets defined 39.3% alpha, 20.1% beta 1388 base pairs and 2110 stacking pairs defined. Time for finding SS restraints: 64.35 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.041A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 36 through 44 removed outlier: 3.867A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.901A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.710A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.809A pdb=" N MET C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.908A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.025A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 4.480A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.659A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.800A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.520A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.948A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 5 through 21 removed outlier: 6.456A pdb=" N GLU F 11 " --> pdb=" O ARG F 7 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.678A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.240A pdb=" N ILE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 4.315A pdb=" N ILE F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP F 147 " --> pdb=" O PHE F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.740A pdb=" N TRP G 62 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.863A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 51 through 59 removed outlier: 4.146A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 12 removed outlier: 3.693A pdb=" N VAL I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN I 12 " --> pdb=" O PRO I 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 7 through 12' Processing helix chain 'I' and resid 24 through 38 removed outlier: 3.769A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 removed outlier: 3.794A pdb=" N ALA I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.698A pdb=" N PHE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 3.668A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 4.445A pdb=" N ARG J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR J 108 " --> pdb=" O ARG J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 103 through 108' Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.847A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 3.711A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 85 removed outlier: 3.983A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 85' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 removed outlier: 4.307A pdb=" N ARG L 57 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.734A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Proline residue: L 126 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 57 removed outlier: 3.648A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU M 49 " --> pdb=" O ARG M 45 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.413A pdb=" N ASN M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.854A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 3 through 23 removed outlier: 3.565A pdb=" N LYS N 13 " --> pdb=" O LEU N 9 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.425A pdb=" N SER N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 16 removed outlier: 4.038A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.404A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 22 Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.772A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.719A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 4.088A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 103 through 118 Processing helix chain 'R' and resid 13 through 25 removed outlier: 3.946A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG R 25 " --> pdb=" O ALA R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.298A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.424A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 3.893A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 5.014A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 57 removed outlier: 4.071A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 63 removed outlier: 4.471A pdb=" N GLU U 62 " --> pdb=" O ASN U 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 2 through 10 removed outlier: 5.099A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 Processing helix chain 'X' and resid 40 through 61 removed outlier: 4.079A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.587A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 18 Processing helix chain 'b' and resid 7 through 15 removed outlier: 7.151A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.331A pdb=" N ILE b 33 " --> pdb=" O MET b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 4.026A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 78 through 90 Processing helix chain 'b' and resid 105 through 126 removed outlier: 4.652A pdb=" N LEU b 109 " --> pdb=" O ASN b 105 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG b 110 " --> pdb=" O TRP b 106 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 150 Processing helix chain 'b' and resid 152 through 157 removed outlier: 4.595A pdb=" N MET b 156 " --> pdb=" O GLY b 152 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY b 157 " --> pdb=" O VAL b 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 152 through 157' Processing helix chain 'b' and resid 167 through 172 removed outlier: 3.608A pdb=" N GLU b 171 " --> pdb=" O ASP b 167 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA b 172 " --> pdb=" O VAL b 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 167 through 172' Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 226 removed outlier: 4.163A pdb=" N GLY b 226 " --> pdb=" O ALA b 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.020A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU c 12 " --> pdb=" O ILE c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 5.011A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.904A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.937A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.252A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.545A pdb=" N LYS c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.440A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 removed outlier: 3.546A pdb=" N VAL d 63 " --> pdb=" O GLU d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.097A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.521A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 108 removed outlier: 3.547A pdb=" N GLY d 108 " --> pdb=" O VAL d 104 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 154 through 168 removed outlier: 3.656A pdb=" N GLU d 162 " --> pdb=" O LYS d 158 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 Proline residue: d 194 - end of helix Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.279A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.360A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.640A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 14 through 33 removed outlier: 3.658A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY f 20 " --> pdb=" O ASP f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.564A pdb=" N LYS g 53 " --> pdb=" O ARG g 49 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS g 55 " --> pdb=" O GLN g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 5.225A pdb=" N SER g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.587A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 113 through 121 Processing helix chain 'i' and resid 32 through 37 Processing helix chain 'i' and resid 39 through 54 Proline residue: i 49 - end of helix removed outlier: 3.589A pdb=" N LEU i 53 " --> pdb=" O PRO i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.937A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 100 removed outlier: 4.781A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.944A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 59 removed outlier: 4.339A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 75 removed outlier: 4.287A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.120A pdb=" N VAL k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.497A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.910A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.818A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASP m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.740A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 33 removed outlier: 5.109A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.782A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 57 Proline residue: n 57 - end of helix Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.119A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS o 47 " --> pdb=" O PHE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.615A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 71 through 82 Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.911A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.036A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.462A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 3.931A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 38 removed outlier: 3.547A pdb=" N VAL u 32 " --> pdb=" O VAL u 28 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS u 34 " --> pdb=" O ALA u 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG u 35 " --> pdb=" O ASP u 31 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TYR u 38 " --> pdb=" O LYS u 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 28 through 38' Processing helix chain 'u' and resid 40 through 64 Processing helix chain 'v' and resid 14 through 30 Processing helix chain 'v' and resid 78 through 102 Processing sheet with id= 1, first strand: chain '0' and resid 2 through 9 removed outlier: 5.819A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '0' and resid 30 through 35 removed outlier: 5.951A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain '3' and resid 13 through 19 removed outlier: 8.274A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.236A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.882A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.742A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU C 164 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.386A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.064A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.521A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR D 46 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE D 35 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 111 through 117 removed outlier: 4.164A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 13, first strand: chain 'D' and resid 25 through 29 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'D' and resid 47 through 52 removed outlier: 4.700A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.483A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.873A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 85 through 92 removed outlier: 5.021A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 19, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 20, first strand: chain 'G' and resid 82 through 89 removed outlier: 5.809A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 22, first strand: chain 'H' and resid 2 through 6 removed outlier: 6.748A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.556A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.083A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 17 through 21 removed outlier: 5.970A pdb=" N ARG J 17 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP J 81 " --> pdb=" O LYS J 66 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS J 66 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.940A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 122 through 125 removed outlier: 3.546A pdb=" N LYS K 143 " --> pdb=" O PHE K 122 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.297A pdb=" N LEU L 103 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'L' and resid 74 through 77 removed outlier: 6.891A pdb=" N ILE L 74 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.233A pdb=" N ARG M 103 " --> pdb=" O ALA M 107 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL M 113 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL M 97 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU M 115 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 50 through 53 Processing sheet with id= 32, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.767A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 52 through 56 removed outlier: 3.996A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG O 56 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.239A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Q' and resid 17 through 21 removed outlier: 4.339A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 37, first strand: chain 'Q' and resid 71 through 78 removed outlier: 4.050A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 39, first strand: chain 'S' and resid 11 through 14 removed outlier: 6.545A pdb=" N GLY S 27 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS S 80 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG S 76 " --> pdb=" O LYS S 65 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 38 through 44 removed outlier: 5.430A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY T 55 " --> pdb=" O GLN T 44 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 8 through 11 Processing sheet with id= 42, first strand: chain 'U' and resid 65 through 68 Processing sheet with id= 43, first strand: chain 'V' and resid 34 through 37 removed outlier: 3.988A pdb=" N ASN V 35 " --> pdb=" O ALA V 61 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN V 50 " --> pdb=" O THR V 62 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 45 through 48 removed outlier: 6.588A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.319A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Y' and resid 32 through 39 removed outlier: 4.292A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS Y 2 " --> pdb=" O ASP Y 39 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Z' and resid 28 through 31 removed outlier: 4.009A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 92 through 95 removed outlier: 3.736A pdb=" N ILE b 166 " --> pdb=" O VAL b 72 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 53 through 59 removed outlier: 3.739A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 164 through 169 removed outlier: 3.617A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'd' and resid 143 through 147 removed outlier: 3.853A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU d 180 " --> pdb=" O VAL d 147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU d 181 " --> pdb=" O ASP d 176 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.863A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.816A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 32 through 39 Processing sheet with id= 55, first strand: chain 'f' and resid 38 through 42 removed outlier: 5.803A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.723A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'g' and resid 73 through 79 removed outlier: 3.792A pdb=" N VAL g 87 " --> pdb=" O LYS g 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.824A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'h' and resid 75 through 78 removed outlier: 5.026A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'i' and resid 3 through 9 removed outlier: 4.072A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 35 through 38 removed outlier: 3.720A pdb=" N GLN j 35 " --> pdb=" O VAL j 77 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.605A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 64, first strand: chain 'k' and resid 29 through 34 removed outlier: 4.124A pdb=" N SER k 108 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 29 through 34 removed outlier: 4.140A pdb=" N SER l 78 " --> pdb=" O CYS l 34 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'l' and resid 35 through 42 removed outlier: 5.702A pdb=" N ALA l 48 " --> pdb=" O PRO l 42 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.668A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 8 through 12 Processing sheet with id= 69, first strand: chain 'q' and resid 20 through 32 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 's' and resid 30 through 34 removed outlier: 4.103A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 1 through 7 removed outlier: 3.834A pdb=" N HIS v 38 " --> pdb=" O ARG v 63 " (cutoff:3.500A) 1931 hydrogen bonds defined for protein. 5727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3476 hydrogen bonds 5448 hydrogen bond angles 0 basepair planarities 1388 basepair parallelities 2110 stacking parallelities Total time for adding SS restraints: 209.28 Time building geometry restraints manager: 58.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13757 1.31 - 1.44: 65572 1.44 - 1.57: 61245 1.57 - 1.70: 8760 1.70 - 1.82: 254 Bond restraints: 149588 Sorted by residual: bond pdb=" C14 YQM A3201 " pdb=" C15 YQM A3201 " ideal model delta sigma weight residual 1.035 1.575 -0.540 2.00e-02 2.50e+03 7.28e+02 bond pdb=" C14 YQM A3202 " pdb=" C15 YQM A3202 " ideal model delta sigma weight residual 1.035 1.568 -0.533 2.00e-02 2.50e+03 7.11e+02 bond pdb=" C08 YQM A3201 " pdb=" C09 YQM A3201 " ideal model delta sigma weight residual 1.951 1.547 0.404 2.00e-02 2.50e+03 4.08e+02 bond pdb=" C08 YQM A3202 " pdb=" C09 YQM A3202 " ideal model delta sigma weight residual 1.951 1.570 0.381 2.00e-02 2.50e+03 3.62e+02 bond pdb=" C15 YQM A3202 " pdb=" C16 YQM A3202 " ideal model delta sigma weight residual 1.771 1.409 0.362 2.00e-02 2.50e+03 3.28e+02 ... (remaining 149583 not shown) Histogram of bond angle deviations from ideal: 90.16 - 101.52: 1763 101.52 - 112.87: 107885 112.87 - 124.23: 94796 124.23 - 135.58: 19172 135.58 - 146.94: 4 Bond angle restraints: 223620 Sorted by residual: angle pdb=" N PRO l 122 " pdb=" CD PRO l 122 " pdb=" CG PRO l 122 " ideal model delta sigma weight residual 103.20 90.16 13.04 1.50e+00 4.44e-01 7.55e+01 angle pdb=" CA PRO l 122 " pdb=" N PRO l 122 " pdb=" CD PRO l 122 " ideal model delta sigma weight residual 112.00 100.67 11.33 1.40e+00 5.10e-01 6.55e+01 angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 146.94 -20.71 3.00e+00 1.11e-01 4.77e+01 angle pdb=" C1' 2MG A2441 " pdb=" N9 2MG A2441 " pdb=" C8 2MG A2441 " ideal model delta sigma weight residual 110.07 128.73 -18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C1' 2MG a1204 " pdb=" N9 2MG a1204 " pdb=" C8 2MG a1204 " ideal model delta sigma weight residual 110.07 128.33 -18.26 3.00e+00 1.11e-01 3.70e+01 ... (remaining 223615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 84689 35.97 - 71.94: 9656 71.94 - 107.91: 1077 107.91 - 143.88: 27 143.88 - 179.86: 69 Dihedral angle restraints: 95518 sinusoidal: 79504 harmonic: 16014 Sorted by residual: dihedral pdb=" O4' U a 205 " pdb=" C1' U a 205 " pdb=" N1 U a 205 " pdb=" C2 U a 205 " ideal model delta sinusoidal sigma weight residual 200.00 20.41 179.59 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2796 " pdb=" C1' U A2796 " pdb=" N1 U A2796 " pdb=" C2 U A2796 " ideal model delta sinusoidal sigma weight residual 200.00 22.12 177.88 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 912 " pdb=" C1' C A 912 " pdb=" N1 C A 912 " pdb=" C2 C A 912 " ideal model delta sinusoidal sigma weight residual 200.00 22.32 177.68 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 95515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 27469 0.081 - 0.162: 1034 0.162 - 0.242: 25 0.242 - 0.323: 3 0.323 - 0.404: 6 Chirality restraints: 28537 Sorted by residual: chirality pdb=" C1* PSU A2576 " pdb=" O4* PSU A2576 " pdb=" C2* PSU A2576 " pdb=" C5 PSU A2576 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C19 YQM A3202 " pdb=" C05 YQM A3202 " pdb=" C17 YQM A3202 " pdb=" C20 YQM A3202 " both_signs ideal model delta sigma weight residual False 2.64 3.01 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C05 YQM A3202 " pdb=" C04 YQM A3202 " pdb=" C06 YQM A3202 " pdb=" C19 YQM A3202 " both_signs ideal model delta sigma weight residual False 2.36 2.71 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 28534 not shown) Planarity restraints: 12110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " 0.057 2.00e-02 2.50e+03 6.05e-01 8.25e+03 pdb=" C4' 7MG A2065 " 0.446 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " 0.671 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " -0.634 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " -0.187 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " 0.966 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " 0.213 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " -0.938 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.048 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' 2MG a1204 " 0.452 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.679 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.615 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.201 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.940 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.211 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.924 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 963 " 0.008 2.00e-02 2.50e+03 5.71e-01 7.33e+03 pdb=" C4' 2MG a 963 " 0.441 2.00e-02 2.50e+03 pdb=" O4' 2MG a 963 " 0.712 2.00e-02 2.50e+03 pdb=" C3' 2MG a 963 " -0.584 2.00e-02 2.50e+03 pdb=" O3' 2MG a 963 " -0.528 2.00e-02 2.50e+03 pdb=" C2' 2MG a 963 " -0.243 2.00e-02 2.50e+03 pdb=" O2' 2MG a 963 " 0.858 2.00e-02 2.50e+03 pdb=" C1' 2MG a 963 " 0.214 2.00e-02 2.50e+03 pdb=" N9 2MG a 963 " -0.877 2.00e-02 2.50e+03 ... (remaining 12107 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 801 2.45 - 3.06: 80311 3.06 - 3.67: 246708 3.67 - 4.29: 386705 4.29 - 4.90: 524292 Nonbonded interactions: 1238817 Sorted by model distance: nonbonded pdb="MG MG a1631 " pdb=" O HOH a1702 " model vdw 1.833 2.170 nonbonded pdb="MG MG A3218 " pdb=" O HOH A3416 " model vdw 1.836 2.170 nonbonded pdb="MG MG a1641 " pdb=" O HOH a1722 " model vdw 1.838 2.170 nonbonded pdb="MG MG a1618 " pdb=" O HOH a1706 " model vdw 1.854 2.170 nonbonded pdb="MG MG a1641 " pdb=" O HOH a1719 " model vdw 1.857 2.170 ... (remaining 1238812 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: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.610 Construct map_model_manager: 0.110 Extract box with map and model: 29.710 Check model and map are aligned: 1.450 Set scattering table: 0.920 Process input model: 495.420 Find NCS groups from input model: 2.640 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:9.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 547.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.540 149588 Z= 0.312 Angle : 0.547 20.710 223620 Z= 0.291 Chirality : 0.034 0.404 28537 Planarity : 0.016 0.605 12110 Dihedral : 22.966 179.855 85202 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.99 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: 1.09 (0.11), residues: 5527 helix: 2.17 (0.12), residues: 1885 sheet: 0.66 (0.15), residues: 1153 loop : -0.35 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 83 HIS 0.007 0.001 HIS f 3 PHE 0.048 0.001 PHE F 138 TYR 0.010 0.001 TYR d 67 ARG 0.021 0.001 ARG b 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1094 time to evaluate : 5.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 ASN cc_start: 0.7762 (t0) cc_final: 0.7435 (t0) REVERT: D 47 GLN cc_start: 0.7125 (mm110) cc_final: 0.6870 (mm110) REVERT: G 141 LEU cc_start: 0.6363 (tp) cc_final: 0.5237 (tp) REVERT: J 70 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7876 (mmm-85) REVERT: S 79 VAL cc_start: 0.8115 (p) cc_final: 0.7780 (t) REVERT: T 68 VAL cc_start: 0.8122 (p) cc_final: 0.7858 (t) REVERT: Z 15 MET cc_start: 0.8690 (mtt) cc_final: 0.8429 (mtt) REVERT: c 21 ASN cc_start: 0.7723 (t0) cc_final: 0.7183 (t0) REVERT: g 65 THR cc_start: 0.7713 (m) cc_final: 0.7480 (m) REVERT: j 17 LEU cc_start: 0.8139 (mt) cc_final: 0.7926 (mp) REVERT: o 12 ILE cc_start: 0.8057 (pt) cc_final: 0.7809 (pp) REVERT: p 54 ILE cc_start: 0.8655 (pt) cc_final: 0.8452 (pp) REVERT: v 29 PHE cc_start: 0.7485 (m-80) cc_final: 0.7182 (m-80) outliers start: 0 outliers final: 2 residues processed: 1094 average time/residue: 2.2081 time to fit residues: 3367.3001 Evaluate side-chains 984 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 982 time to evaluate : 5.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain b residue 53 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 825 optimal weight: 0.0770 chunk 741 optimal weight: 20.0000 chunk 411 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 500 optimal weight: 4.9990 chunk 396 optimal weight: 9.9990 chunk 766 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 466 optimal weight: 3.9990 chunk 570 optimal weight: 9.9990 chunk 888 optimal weight: 7.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 4 GLN 3 35 GLN 3 37 GLN C 86 ASN C 90 HIS C 120 ASN C 185 HIS C 201 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 115 GLN D 153 GLN D 167 HIS E 40 GLN I 58 ASN I 136 GLN J 3 GLN J 82 ASN M 5 ASN M 23 ASN O 44 GLN P 37 GLN Q 12 HIS Q 82 HIS R 37 ASN T 47 ASN U 84 HIS W 17 ASN Z 25 ASN Z 37 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 ASN c 49 ASN e 85 ASN e 88 HIS f 3 HIS ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 4 GLN h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 79 HIS k 23 HIS m 105 ASN o 40 GLN p 44 ASN r 52 GLN s 69 HIS s 83 HIS t 3 ASN t 20 HIS v 13 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 149588 Z= 0.477 Angle : 0.879 17.501 223620 Z= 0.442 Chirality : 0.050 0.455 28537 Planarity : 0.007 0.130 12110 Dihedral : 23.688 179.698 74237 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.75 % Favored : 96.07 % Rotamer: Outliers : 3.06 % Allowed : 11.89 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 5527 helix: 1.37 (0.12), residues: 1884 sheet: 0.55 (0.15), residues: 1071 loop : -0.70 (0.11), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP b 106 HIS 0.016 0.002 HIS M 16 PHE 0.033 0.003 PHE F 138 TYR 0.025 0.003 TYR r 70 ARG 0.021 0.001 ARG b 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 994 time to evaluate : 5.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 ASN cc_start: 0.8046 (t0) cc_final: 0.7701 (t0) REVERT: C 82 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6859 (mt-10) REVERT: C 101 ARG cc_start: 0.8039 (mtt90) cc_final: 0.7834 (mtt90) REVERT: C 181 MET cc_start: 0.4949 (mtm) cc_final: 0.4689 (mtt) REVERT: C 214 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6199 (mtt-85) REVERT: F 26 MET cc_start: 0.5305 (ttp) cc_final: 0.5024 (ttp) REVERT: F 34 ILE cc_start: 0.5663 (OUTLIER) cc_final: 0.5250 (mm) REVERT: G 141 LEU cc_start: 0.6271 (tp) cc_final: 0.6023 (tt) REVERT: I 73 LYS cc_start: 0.8067 (mptp) cc_final: 0.7844 (mptp) REVERT: L 41 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6383 (ttp-170) REVERT: L 96 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7106 (mp0) REVERT: P 93 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.7229 (ttp80) REVERT: R 33 LEU cc_start: 0.7990 (mm) cc_final: 0.7788 (mm) REVERT: R 42 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7926 (tttt) REVERT: S 79 VAL cc_start: 0.8177 (p) cc_final: 0.7899 (t) REVERT: U 91 MET cc_start: 0.7770 (mtt) cc_final: 0.7554 (mtt) REVERT: W 11 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7735 (mtt-85) REVERT: W 28 ARG cc_start: 0.8224 (mtm180) cc_final: 0.7919 (mtp-110) REVERT: c 21 ASN cc_start: 0.7622 (t0) cc_final: 0.7175 (t0) REVERT: d 54 SER cc_start: 0.7873 (t) cc_final: 0.7588 (m) REVERT: k 25 SER cc_start: 0.7164 (t) cc_final: 0.6947 (p) REVERT: o 12 ILE cc_start: 0.8144 (pt) cc_final: 0.7902 (pp) REVERT: v 4 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5855 (mp0) outliers start: 140 outliers final: 68 residues processed: 1042 average time/residue: 2.2129 time to fit residues: 3206.3901 Evaluate side-chains 1031 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 958 time to evaluate : 5.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ARG Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain R residue 42 LYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 73 GLN Chi-restraints excluded: chain d residue 92 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 143 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 126 SER Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 77 ARG Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 71 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain v residue 4 GLU Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 79 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 493 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 739 optimal weight: 1.9990 chunk 604 optimal weight: 50.0000 chunk 244 optimal weight: 4.9990 chunk 889 optimal weight: 1.9990 chunk 961 optimal weight: 2.9990 chunk 792 optimal weight: 0.0980 chunk 882 optimal weight: 3.9990 chunk 303 optimal weight: 0.1980 chunk 713 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN E 40 GLN I 58 ASN M 23 ASN M 26 ASN O 55 ASN O 78 GLN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 HIS h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN o 40 GLN p 84 GLN r 52 GLN t 3 ASN v 13 ASN v 78 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 149588 Z= 0.151 Angle : 0.605 13.931 223620 Z= 0.324 Chirality : 0.036 0.396 28537 Planarity : 0.005 0.123 12110 Dihedral : 23.375 179.884 74233 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.84 % Favored : 97.00 % Rotamer: Outliers : 2.62 % Allowed : 15.12 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.11), residues: 5527 helix: 1.88 (0.12), residues: 1893 sheet: 0.62 (0.15), residues: 1097 loop : -0.52 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP c 201 HIS 0.005 0.001 HIS b 41 PHE 0.019 0.001 PHE F 138 TYR 0.016 0.001 TYR Q 2 ARG 0.026 0.001 ARG b 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1000 time to evaluate : 5.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6790 (mmp-170) REVERT: C 38 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7065 (mmtm) REVERT: D 172 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7197 (ttt90) REVERT: F 72 LYS cc_start: 0.4433 (ptpt) cc_final: 0.4031 (pttm) REVERT: F 141 ILE cc_start: 0.4056 (pt) cc_final: 0.3748 (mp) REVERT: G 141 LEU cc_start: 0.6214 (tp) cc_final: 0.5977 (tt) REVERT: G 167 GLU cc_start: 0.4722 (pt0) cc_final: 0.4516 (tt0) REVERT: I 85 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7749 (mttp) REVERT: I 118 MET cc_start: 0.8474 (mtt) cc_final: 0.8264 (mtp) REVERT: J 70 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7931 (mmm-85) REVERT: L 41 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6391 (ttp-170) REVERT: L 96 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7166 (mp0) REVERT: P 93 ARG cc_start: 0.7461 (ttp-170) cc_final: 0.7240 (ttp80) REVERT: S 44 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7774 (mtpp) REVERT: S 79 VAL cc_start: 0.8159 (p) cc_final: 0.7930 (t) REVERT: U 46 LEU cc_start: 0.8106 (mt) cc_final: 0.7803 (mm) REVERT: W 11 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7602 (mtt-85) REVERT: d 34 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6470 (tttm) REVERT: d 54 SER cc_start: 0.7766 (t) cc_final: 0.7484 (m) REVERT: d 64 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7384 (ttp80) REVERT: d 71 GLU cc_start: 0.7695 (tp30) cc_final: 0.7440 (tp30) REVERT: j 7 ARG cc_start: 0.6349 (ttm170) cc_final: 0.6057 (ttm170) REVERT: m 72 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6291 (tt0) REVERT: o 12 ILE cc_start: 0.8033 (pt) cc_final: 0.7823 (pp) REVERT: p 81 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6917 (mm-40) outliers start: 120 outliers final: 49 residues processed: 1035 average time/residue: 2.2821 time to fit residues: 3282.3727 Evaluate side-chains 1033 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 976 time to evaluate : 5.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ARG Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 139 PRO Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 34 LYS Chi-restraints excluded: chain d residue 64 ARG Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 72 GLU Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 71 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 79 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 879 optimal weight: 10.0000 chunk 668 optimal weight: 7.9990 chunk 461 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 chunk 597 optimal weight: 6.9990 chunk 892 optimal weight: 0.9980 chunk 945 optimal weight: 3.9990 chunk 466 optimal weight: 7.9990 chunk 846 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN C 201 ASN D 37 GLN D 153 GLN E 96 ASN I 58 ASN I 95 HIS M 23 ASN M 26 ASN O 78 GLN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 205 ASN c 21 ASN c 88 GLN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 86 GLN k 28 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN r 52 GLN t 3 ASN v 13 ASN v 78 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 149588 Z= 0.328 Angle : 0.728 16.513 223620 Z= 0.375 Chirality : 0.042 0.444 28537 Planarity : 0.007 0.134 12110 Dihedral : 23.435 179.917 74233 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.60 % Favored : 96.24 % Rotamer: Outliers : 3.88 % Allowed : 15.84 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 5527 helix: 1.63 (0.12), residues: 1878 sheet: 0.55 (0.15), residues: 1100 loop : -0.66 (0.11), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP s 34 HIS 0.009 0.001 HIS M 16 PHE 0.028 0.002 PHE v 29 TYR 0.019 0.002 TYR Q 2 ARG 0.015 0.001 ARG b 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 986 time to evaluate : 5.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7205 (mmtm) REVERT: F 38 MET cc_start: 0.5332 (ppp) cc_final: 0.4529 (pmt) REVERT: F 141 ILE cc_start: 0.3715 (pt) cc_final: 0.3276 (OUTLIER) REVERT: G 141 LEU cc_start: 0.6257 (tp) cc_final: 0.5994 (tt) REVERT: G 167 GLU cc_start: 0.4724 (pt0) cc_final: 0.4481 (tt0) REVERT: I 85 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7753 (mttp) REVERT: L 41 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6389 (ttp-170) REVERT: L 51 ARG cc_start: 0.6795 (ptm-80) cc_final: 0.6436 (ptm-80) REVERT: L 96 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7161 (mp0) REVERT: P 93 ARG cc_start: 0.7469 (ttp-170) cc_final: 0.7130 (ttp80) REVERT: S 79 VAL cc_start: 0.8115 (p) cc_final: 0.7870 (t) REVERT: W 11 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7698 (mtt-85) REVERT: b 205 ASN cc_start: 0.5296 (t0) cc_final: 0.5052 (t160) REVERT: d 14 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7230 (mmt-90) REVERT: d 54 SER cc_start: 0.7826 (t) cc_final: 0.7576 (m) REVERT: d 64 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7546 (ttp80) REVERT: d 93 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7642 (mm) REVERT: d 97 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6511 (mm-30) REVERT: j 7 ARG cc_start: 0.6374 (ttm170) cc_final: 0.5871 (ttm-80) REVERT: o 12 ILE cc_start: 0.8137 (pt) cc_final: 0.7920 (pp) REVERT: p 81 GLN cc_start: 0.7297 (mm-40) cc_final: 0.7045 (mt0) REVERT: q 76 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7439 (tp) outliers start: 178 outliers final: 102 residues processed: 1053 average time/residue: 2.2116 time to fit residues: 3249.4642 Evaluate side-chains 1076 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 968 time to evaluate : 5.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ARG Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain S residue 32 LYS Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 31 GLU Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 64 ARG Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 147 THR Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 113 THR Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 19 MET Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 71 THR Chi-restraints excluded: chain q residue 76 LEU Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 787 optimal weight: 5.9990 chunk 536 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 703 optimal weight: 1.9990 chunk 390 optimal weight: 50.0000 chunk 806 optimal weight: 0.9980 chunk 653 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 482 optimal weight: 9.9990 chunk 848 optimal weight: 0.7980 chunk 238 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS C 25 HIS E 23 ASN I 58 ASN M 23 ASN M 26 ASN O 78 GLN P 37 GLN P 56 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 122 GLN b 192 ASN b 197 ASN c 21 ASN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN s 65 HIS t 3 ASN v 78 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 149588 Z= 0.185 Angle : 0.618 14.477 223620 Z= 0.329 Chirality : 0.036 0.407 28537 Planarity : 0.006 0.126 12110 Dihedral : 23.321 179.809 74233 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.06 % Favored : 96.82 % Rotamer: Outliers : 3.91 % Allowed : 17.09 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.11), residues: 5527 helix: 1.82 (0.12), residues: 1879 sheet: 0.62 (0.15), residues: 1126 loop : -0.57 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 201 HIS 0.006 0.001 HIS b 41 PHE 0.018 0.001 PHE v 29 TYR 0.016 0.001 TYR Q 2 ARG 0.013 0.000 ARG b 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 993 time to evaluate : 5.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6816 (mmp-170) REVERT: C 38 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7147 (mmtm) REVERT: D 172 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7219 (ttt90) REVERT: F 38 MET cc_start: 0.5227 (ppp) cc_final: 0.4787 (pmt) REVERT: G 167 GLU cc_start: 0.4687 (pt0) cc_final: 0.4448 (tt0) REVERT: I 85 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7707 (mttp) REVERT: L 41 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6366 (ttp-170) REVERT: L 96 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7129 (mp0) REVERT: L 128 LYS cc_start: 0.6449 (mmpt) cc_final: 0.6236 (mmpt) REVERT: P 93 ARG cc_start: 0.7467 (ttp80) cc_final: 0.7105 (ttp80) REVERT: R 33 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7655 (mm) REVERT: S 79 VAL cc_start: 0.8099 (p) cc_final: 0.7856 (t) REVERT: U 46 LEU cc_start: 0.8092 (mt) cc_final: 0.7817 (mm) REVERT: W 11 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7638 (mtt-85) REVERT: b 131 LEU cc_start: 0.4148 (OUTLIER) cc_final: 0.3941 (tt) REVERT: b 205 ASN cc_start: 0.5253 (t0) cc_final: 0.4988 (t160) REVERT: d 55 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6497 (mp) REVERT: d 64 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7491 (ttp80) REVERT: d 93 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7610 (mm) REVERT: e 51 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7202 (mtpp) REVERT: m 72 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6297 (tt0) REVERT: o 12 ILE cc_start: 0.8091 (pt) cc_final: 0.7886 (pp) REVERT: p 81 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6836 (mm-40) REVERT: q 28 ARG cc_start: 0.6048 (OUTLIER) cc_final: 0.5814 (ptm-80) outliers start: 179 outliers final: 91 residues processed: 1061 average time/residue: 2.1995 time to fit residues: 3265.9622 Evaluate side-chains 1074 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 970 time to evaluate : 5.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ARG Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 32 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 64 ARG Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 113 THR Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 72 GLU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 71 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 79 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 318 optimal weight: 4.9990 chunk 851 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 555 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 946 optimal weight: 0.8980 chunk 785 optimal weight: 2.9990 chunk 438 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 313 optimal weight: 0.8980 chunk 496 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 ASN D 37 GLN E 23 ASN I 58 ASN M 23 ASN M 26 ASN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 192 ASN c 21 ASN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 86 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN r 52 GLN s 65 HIS t 3 ASN v 78 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 149588 Z= 0.307 Angle : 0.711 16.450 223620 Z= 0.368 Chirality : 0.041 0.432 28537 Planarity : 0.006 0.134 12110 Dihedral : 23.395 179.962 74233 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 4.43 % Allowed : 17.70 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.11), residues: 5527 helix: 1.57 (0.12), residues: 1877 sheet: 0.53 (0.15), residues: 1114 loop : -0.70 (0.11), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP s 34 HIS 0.008 0.001 HIS j 15 PHE 0.022 0.002 PHE s 10 TYR 0.018 0.002 TYR r 32 ARG 0.011 0.001 ARG b 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 966 time to evaluate : 5.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7145 (mmtm) REVERT: C 53 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6956 (m170) REVERT: D 172 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7228 (ttt90) REVERT: G 141 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.6063 (tp) REVERT: G 167 GLU cc_start: 0.4717 (pt0) cc_final: 0.4384 (tt0) REVERT: I 23 LYS cc_start: 0.7852 (mtpp) cc_final: 0.7601 (ptpt) REVERT: I 79 GLU cc_start: 0.6083 (mm-30) cc_final: 0.5737 (mp0) REVERT: I 85 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7731 (mttp) REVERT: J 45 GLU cc_start: 0.6135 (tp30) cc_final: 0.5710 (tp30) REVERT: L 1 MET cc_start: 0.6608 (mmt) cc_final: 0.6149 (mmt) REVERT: L 41 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6393 (ttp-170) REVERT: L 96 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7127 (mp0) REVERT: P 93 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7217 (ttp80) REVERT: P 100 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7993 (ttt) REVERT: U 91 MET cc_start: 0.7613 (mtt) cc_final: 0.7377 (mtt) REVERT: W 11 ARG cc_start: 0.7943 (mtp180) cc_final: 0.7692 (mtt-85) REVERT: W 28 ARG cc_start: 0.8184 (mtm180) cc_final: 0.7899 (mtp-110) REVERT: c 58 GLU cc_start: 0.6836 (tp30) cc_final: 0.6454 (tp30) REVERT: d 14 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6367 (tpm170) REVERT: d 55 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6598 (mp) REVERT: d 63 VAL cc_start: 0.8848 (t) cc_final: 0.8630 (t) REVERT: d 64 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7458 (ttt90) REVERT: d 93 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7606 (mm) REVERT: f 74 LEU cc_start: 0.8755 (mt) cc_final: 0.8551 (mt) REVERT: j 7 ARG cc_start: 0.6314 (ttm170) cc_final: 0.6104 (ttm-80) REVERT: m 72 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6423 (tt0) REVERT: o 12 ILE cc_start: 0.8145 (pt) cc_final: 0.7935 (pp) REVERT: p 81 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6847 (mm-40) outliers start: 203 outliers final: 130 residues processed: 1050 average time/residue: 2.2070 time to fit residues: 3234.0965 Evaluate side-chains 1100 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 958 time to evaluate : 5.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ARG Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 72 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 147 GLU Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 64 ARG Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 98 SER Chi-restraints excluded: chain d residue 121 SER Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 113 THR Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 72 GLU Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 19 MET Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 71 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain u residue 63 GLU Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 912 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 539 optimal weight: 0.3980 chunk 691 optimal weight: 4.9990 chunk 535 optimal weight: 20.0000 chunk 796 optimal weight: 30.0000 chunk 528 optimal weight: 5.9990 chunk 942 optimal weight: 1.9990 chunk 589 optimal weight: 5.9990 chunk 574 optimal weight: 9.9990 chunk 435 optimal weight: 0.0040 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN E 23 ASN I 58 ASN M 23 ASN M 26 ASN O 78 GLN P 37 GLN R 61 ASN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN e 85 ASN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN r 52 GLN s 65 HIS t 3 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 149588 Z= 0.202 Angle : 0.629 14.749 223620 Z= 0.334 Chirality : 0.037 0.407 28537 Planarity : 0.006 0.127 12110 Dihedral : 23.310 179.980 74233 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.38 % Favored : 96.47 % Rotamer: Outliers : 3.80 % Allowed : 18.90 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 5527 helix: 1.77 (0.12), residues: 1869 sheet: 0.53 (0.15), residues: 1135 loop : -0.63 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 201 HIS 0.005 0.001 HIS j 15 PHE 0.018 0.001 PHE c 130 TYR 0.016 0.002 TYR Q 2 ARG 0.011 0.000 ARG S 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 972 time to evaluate : 9.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6816 (mmp-170) REVERT: C 38 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7194 (mmtm) REVERT: C 53 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.6837 (m170) REVERT: D 29 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6614 (mt-10) REVERT: D 172 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7232 (ttt90) REVERT: G 141 LEU cc_start: 0.6313 (tt) cc_final: 0.6001 (tp) REVERT: G 167 GLU cc_start: 0.4731 (pt0) cc_final: 0.4406 (tt0) REVERT: I 23 LYS cc_start: 0.7857 (mtpp) cc_final: 0.7617 (ptpt) REVERT: I 79 GLU cc_start: 0.6111 (mm-30) cc_final: 0.5722 (mp0) REVERT: I 85 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7685 (mttp) REVERT: L 1 MET cc_start: 0.6629 (mmt) cc_final: 0.6264 (mmt) REVERT: L 41 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6376 (ttp-170) REVERT: L 51 ARG cc_start: 0.6831 (ptm-80) cc_final: 0.6278 (ptm-80) REVERT: L 96 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7133 (mp0) REVERT: P 93 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7214 (ttp80) REVERT: P 100 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8001 (ttt) REVERT: R 106 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7797 (mttp) REVERT: S 79 VAL cc_start: 0.8171 (p) cc_final: 0.7541 (t) REVERT: U 46 LEU cc_start: 0.8130 (mt) cc_final: 0.7865 (mm) REVERT: W 11 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7653 (mtt-85) REVERT: d 14 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7198 (mmt-90) REVERT: d 55 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6544 (mp) REVERT: d 63 VAL cc_start: 0.8831 (t) cc_final: 0.8618 (t) REVERT: d 64 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7436 (ttp80) REVERT: d 93 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7593 (mm) REVERT: e 19 ARG cc_start: 0.7649 (tmm-80) cc_final: 0.7261 (tmm-80) REVERT: h 22 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7828 (mtpp) REVERT: m 72 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6319 (tt0) REVERT: o 12 ILE cc_start: 0.8101 (pt) cc_final: 0.7898 (pp) REVERT: p 81 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6854 (mm-40) outliers start: 174 outliers final: 116 residues processed: 1043 average time/residue: 2.2456 time to fit residues: 3284.0843 Evaluate side-chains 1088 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 958 time to evaluate : 5.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ARG Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 83 TRP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 147 GLU Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 187 MET Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 64 ARG Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 121 SER Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 113 THR Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 72 GLU Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 71 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain u residue 63 GLU Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 79 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 583 optimal weight: 5.9990 chunk 376 optimal weight: 6.9990 chunk 562 optimal weight: 4.9990 chunk 283 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 599 optimal weight: 10.0000 chunk 642 optimal weight: 5.9990 chunk 466 optimal weight: 0.1980 chunk 87 optimal weight: 7.9990 chunk 740 optimal weight: 0.7980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 35 GLN C 201 ASN D 37 GLN E 23 ASN I 58 ASN M 23 ASN M 26 ASN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN e 85 ASN ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 86 GLN k 107 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN r 52 GLN s 65 HIS t 3 ASN ** v 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 149588 Z= 0.390 Angle : 0.783 17.025 223620 Z= 0.398 Chirality : 0.045 0.444 28537 Planarity : 0.007 0.136 12110 Dihedral : 23.457 179.812 74233 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.05 % Favored : 95.78 % Rotamer: Outliers : 4.23 % Allowed : 19.14 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5527 helix: 1.39 (0.12), residues: 1875 sheet: 0.46 (0.15), residues: 1117 loop : -0.84 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP s 34 HIS 0.009 0.001 HIS f 3 PHE 0.026 0.002 PHE v 29 TYR 0.019 0.002 TYR r 70 ARG 0.013 0.001 ARG S 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 963 time to evaluate : 5.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7159 (mmtm) REVERT: C 53 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.7017 (m90) REVERT: C 177 ARG cc_start: 0.5798 (mmm-85) cc_final: 0.5579 (mmm-85) REVERT: D 29 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6728 (mt-10) REVERT: D 172 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7238 (ttt90) REVERT: G 167 GLU cc_start: 0.4804 (pt0) cc_final: 0.4381 (tt0) REVERT: I 85 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7754 (mttp) REVERT: L 41 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6309 (ttp-170) REVERT: L 51 ARG cc_start: 0.6930 (ptm-80) cc_final: 0.6521 (ptm-80) REVERT: L 96 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7123 (mp0) REVERT: P 100 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7984 (ttt) REVERT: R 106 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7895 (mttp) REVERT: W 11 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7711 (mtt-85) REVERT: b 12 LEU cc_start: 0.4344 (pp) cc_final: 0.4023 (mp) REVERT: d 14 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6185 (tpm170) REVERT: d 54 SER cc_start: 0.7920 (t) cc_final: 0.7650 (m) REVERT: d 55 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6689 (mp) REVERT: d 64 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7461 (ttt90) REVERT: d 93 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7597 (mm) REVERT: h 22 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7896 (mtpp) REVERT: o 12 ILE cc_start: 0.8168 (pt) cc_final: 0.7956 (pp) REVERT: p 81 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6902 (mm-40) outliers start: 194 outliers final: 132 residues processed: 1047 average time/residue: 2.1925 time to fit residues: 3213.1561 Evaluate side-chains 1103 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 959 time to evaluate : 5.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ARG Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain I residue 120 LYS Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 80 MET Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain X residue 30 MET Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 147 GLU Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 187 MET Chi-restraints excluded: chain d residue 12 SER Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 64 ARG Chi-restraints excluded: chain d residue 66 ILE Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 121 SER Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain f residue 9 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 113 THR Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 71 THR Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain u residue 63 GLU Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 79 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 857 optimal weight: 0.5980 chunk 903 optimal weight: 0.6980 chunk 823 optimal weight: 0.8980 chunk 878 optimal weight: 6.9990 chunk 902 optimal weight: 0.7980 chunk 528 optimal weight: 7.9990 chunk 382 optimal weight: 10.0000 chunk 689 optimal weight: 0.5980 chunk 269 optimal weight: 7.9990 chunk 793 optimal weight: 30.0000 chunk 830 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN E 23 ASN I 58 ASN M 23 ASN M 26 ASN O 55 ASN O 78 GLN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 ASN c 21 ASN c 88 GLN e 85 ASN g 142 HIS h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN s 57 HIS s 65 HIS t 3 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 149588 Z= 0.133 Angle : 0.593 13.390 223620 Z= 0.318 Chirality : 0.035 0.397 28537 Planarity : 0.005 0.121 12110 Dihedral : 23.244 179.907 74233 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.99 % Favored : 96.85 % Rotamer: Outliers : 2.79 % Allowed : 20.76 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.11), residues: 5527 helix: 1.87 (0.12), residues: 1867 sheet: 0.61 (0.15), residues: 1121 loop : -0.63 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 83 HIS 0.005 0.001 HIS b 41 PHE 0.015 0.001 PHE Q 93 TYR 0.015 0.001 TYR Q 2 ARG 0.013 0.000 ARG J 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 967 time to evaluate : 5.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6819 (mmp-170) REVERT: 1 25 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7006 (ttmt) REVERT: C 38 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7148 (mmtm) REVERT: C 161 SER cc_start: 0.7385 (OUTLIER) cc_final: 0.6974 (t) REVERT: C 181 MET cc_start: 0.4180 (ptp) cc_final: 0.3769 (mtt) REVERT: D 29 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6669 (mt-10) REVERT: D 172 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7222 (ttt90) REVERT: F 38 MET cc_start: 0.5237 (ppp) cc_final: 0.4335 (pmm) REVERT: F 167 ARG cc_start: 0.3380 (mmp-170) cc_final: 0.3151 (mmp80) REVERT: G 149 ARG cc_start: 0.7483 (ttt90) cc_final: 0.7215 (ttt90) REVERT: G 167 GLU cc_start: 0.4744 (pt0) cc_final: 0.4438 (tt0) REVERT: I 23 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7556 (ptpt) REVERT: I 79 GLU cc_start: 0.6040 (mm-30) cc_final: 0.5668 (mp0) REVERT: L 41 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6380 (ttp-170) REVERT: L 96 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7132 (mp0) REVERT: P 100 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7974 (ttt) REVERT: S 44 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7755 (mtpp) REVERT: U 46 LEU cc_start: 0.8107 (mt) cc_final: 0.7885 (mm) REVERT: W 11 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7616 (mtp-110) REVERT: b 12 LEU cc_start: 0.4305 (pp) cc_final: 0.4008 (mp) REVERT: c 58 GLU cc_start: 0.6859 (tp30) cc_final: 0.6413 (tp30) REVERT: d 55 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6459 (mp) REVERT: d 64 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7493 (ttp80) REVERT: d 71 GLU cc_start: 0.7649 (tp30) cc_final: 0.7341 (tp30) REVERT: d 93 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7468 (mm) REVERT: h 22 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7789 (mtpp) REVERT: m 72 GLU cc_start: 0.6519 (tm-30) cc_final: 0.6243 (tt0) REVERT: p 81 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6827 (mm-40) outliers start: 128 outliers final: 86 residues processed: 1021 average time/residue: 2.2463 time to fit residues: 3205.5187 Evaluate side-chains 1054 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 957 time to evaluate : 5.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ARG Chi-restraints excluded: chain 1 residue 10 LEU Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 90 LYS Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 147 GLU Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 187 MET Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 64 ARG Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 121 SER Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 113 THR Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain u residue 63 GLU Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 875 optimal weight: 5.9990 chunk 576 optimal weight: 1.9990 chunk 928 optimal weight: 8.9990 chunk 566 optimal weight: 1.9990 chunk 440 optimal weight: 5.9990 chunk 645 optimal weight: 5.9990 chunk 974 optimal weight: 0.6980 chunk 896 optimal weight: 1.9990 chunk 775 optimal weight: 0.2980 chunk 80 optimal weight: 7.9990 chunk 599 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 ASN D 37 GLN I 58 ASN M 23 ASN M 26 ASN O 55 ASN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 ASN c 21 ASN e 85 ASN f 87 ASN g 142 HIS h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN r 52 GLN s 65 HIS t 3 ASN ** v 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 149588 Z= 0.182 Angle : 0.613 14.378 223620 Z= 0.325 Chirality : 0.036 0.407 28537 Planarity : 0.006 0.126 12110 Dihedral : 23.222 179.921 74233 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.49 % Favored : 96.35 % Rotamer: Outliers : 2.55 % Allowed : 21.48 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.11), residues: 5527 helix: 1.83 (0.12), residues: 1873 sheet: 0.61 (0.15), residues: 1136 loop : -0.63 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 98 HIS 0.005 0.001 HIS j 15 PHE 0.018 0.001 PHE v 29 TYR 0.016 0.001 TYR Q 2 ARG 0.014 0.001 ARG D 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11054 Ramachandran restraints generated. 5527 Oldfield, 0 Emsley, 5527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 953 time to evaluate : 5.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6808 (mmp-170) REVERT: C 38 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7134 (mmtm) REVERT: D 29 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6637 (mt-10) REVERT: D 172 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7256 (ttt90) REVERT: F 38 MET cc_start: 0.5067 (ppp) cc_final: 0.4275 (pmt) REVERT: G 141 LEU cc_start: 0.6206 (tp) cc_final: 0.5827 (tp) REVERT: G 167 GLU cc_start: 0.4808 (pt0) cc_final: 0.4498 (tt0) REVERT: I 23 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7581 (ptpt) REVERT: I 79 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5699 (mp0) REVERT: I 85 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7679 (mttp) REVERT: L 41 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6411 (ttp-170) REVERT: L 96 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7139 (mp0) REVERT: P 100 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7982 (ttt) REVERT: U 46 LEU cc_start: 0.8118 (mt) cc_final: 0.7875 (mm) REVERT: W 11 ARG cc_start: 0.7835 (mtp180) cc_final: 0.7609 (mtp-110) REVERT: b 12 LEU cc_start: 0.4365 (pp) cc_final: 0.4084 (mp) REVERT: d 15 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: d 55 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6501 (mp) REVERT: d 63 VAL cc_start: 0.8868 (t) cc_final: 0.8569 (t) REVERT: d 64 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7543 (ttt90) REVERT: d 71 GLU cc_start: 0.7714 (tp30) cc_final: 0.7463 (tp30) REVERT: d 93 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7585 (mm) REVERT: h 22 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7795 (mtpp) REVERT: m 27 ARG cc_start: 0.7315 (ttm110) cc_final: 0.6992 (ttm170) REVERT: m 72 GLU cc_start: 0.6556 (tm-30) cc_final: 0.6287 (tt0) REVERT: p 81 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6834 (mm-40) outliers start: 117 outliers final: 87 residues processed: 1005 average time/residue: 2.2132 time to fit residues: 3108.4194 Evaluate side-chains 1049 residues out of total 4582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 951 time to evaluate : 5.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 40 ARG Chi-restraints excluded: chain 1 residue 25 LYS Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 85 LYS Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 90 LYS Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 6 LYS Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain b residue 80 ASN Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 147 GLU Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 186 THR Chi-restraints excluded: chain c residue 187 MET Chi-restraints excluded: chain d residue 15 GLU Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 64 ARG Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 121 SER Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 22 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 113 THR Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 37 CYS Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain m residue 7 VAL Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain u residue 63 GLU Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 475 optimal weight: 0.6980 chunk 616 optimal weight: 5.9990 chunk 826 optimal weight: 0.6980 chunk 237 optimal weight: 8.9990 chunk 715 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 777 optimal weight: 3.9990 chunk 325 optimal weight: 0.0870 chunk 797 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 4 GLN D 37 GLN E 23 ASN I 58 ASN M 23 ASN M 26 ASN O 78 GLN P 37 GLN W 17 ASN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 88 GLN f 87 ASN g 142 HIS h 41 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 62 GLN r 52 GLN s 65 HIS t 3 ASN ** v 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.156613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138517 restraints weight = 198650.481| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 0.69 r_work: 0.3323 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 149588 Z= 0.206 Angle : 0.632 18.730 223620 Z= 0.333 Chirality : 0.036 0.405 28537 Planarity : 0.006 0.127 12110 Dihedral : 23.232 179.947 74233 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.55 % Favored : 96.29 % Rotamer: Outliers : 2.84 % Allowed : 21.34 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 5527 helix: 1.79 (0.12), residues: 1868 sheet: 0.57 (0.15), residues: 1138 loop : -0.67 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 83 HIS 0.006 0.001 HIS j 15 PHE 0.018 0.002 PHE Q 93 TYR 0.016 0.002 TYR Q 2 ARG 0.016 0.001 ARG J 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43147.03 seconds wall clock time: 746 minutes 27.08 seconds (44787.08 seconds total)