Starting phenix.real_space_refine on Fri Feb 23 13:17:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crx_26959/02_2024/8crx_26959_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crx_26959/02_2024/8crx_26959.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crx_26959/02_2024/8crx_26959_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crx_26959/02_2024/8crx_26959_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crx_26959/02_2024/8crx_26959_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crx_26959/02_2024/8crx_26959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crx_26959/02_2024/8crx_26959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crx_26959/02_2024/8crx_26959_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crx_26959/02_2024/8crx_26959_updated.pdb" } resolution = 2.78 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= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 4620 5.49 5 Mg 386 5.21 5 S 156 5.16 5 C 72109 2.51 5 N 26779 2.21 5 O 40551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H ASP 118": "OD1" <-> "OD2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "L ASP 14": "OD1" <-> "OD2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q GLU 7": "OE1" <-> "OE2" Residue "Q ASP 22": "OD1" <-> "OD2" Residue "Q ASP 55": "OD1" <-> "OD2" Residue "R ASP 25": "OD1" <-> "OD2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "T ASP 59": "OD1" <-> "OD2" Residue "P GLU 35": "OE1" <-> "OE2" Residue "P ASP 52": "OD1" <-> "OD2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "P ASP 113": "OD1" <-> "OD2" Residue "P GLU 114": "OE1" <-> "OE2" Residue "P GLU 125": "OE1" <-> "OE2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G ASP 182": "OD1" <-> "OD2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J ASP 133": "OD1" <-> "OD2" Residue "J ASP 150": "OD1" <-> "OD2" Residue "J TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "N ASP 12": "OD1" <-> "OD2" Residue "N ASP 69": "OD1" <-> "OD2" Residue "N ASP 77": "OD1" <-> "OD2" Residue "U GLU 73": "OE1" <-> "OE2" Residue "c ASP 20": "OD1" <-> "OD2" Residue "c ASP 66": "OD1" <-> "OD2" Residue "c ASP 71": "OD1" <-> "OD2" Residue "c ASP 109": "OD1" <-> "OD2" Residue "c ASP 186": "OD1" <-> "OD2" Residue "c ASP 230": "OD1" <-> "OD2" Residue "c GLU 237": "OE1" <-> "OE2" Residue "d GLU 4": "OE1" <-> "OE2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d GLU 174": "OE1" <-> "OE2" Residue "e ASP 25": "OD1" <-> "OD2" Residue "e GLU 152": "OE1" <-> "OE2" Residue "f GLU 41": "OE1" <-> "OE2" Residue "f TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 54": "OE1" <-> "OE2" Residue "g ASP 57": "OD1" <-> "OD2" Residue "g ASP 139": "OD1" <-> "OD2" Residue "g TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 19": "OD1" <-> "OD2" Residue "i ASP 71": "OD1" <-> "OD2" Residue "j PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "m GLU 17": "OE1" <-> "OE2" Residue "m ASP 91": "OD1" <-> "OD2" Residue "n PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 103": "OD1" <-> "OD2" Residue "n ASP 126": "OD1" <-> "OD2" Residue "p ASP 49": "OD1" <-> "OD2" Residue "p GLU 97": "OE1" <-> "OE2" Residue "r ASP 48": "OD1" <-> "OD2" Residue "r ASP 85": "OD1" <-> "OD2" Residue "s ASP 8": "OD1" <-> "OD2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 80": "OD1" <-> "OD2" Residue "t ASP 10": "OD1" <-> "OD2" Residue "t ASP 30": "OD1" <-> "OD2" Residue "t GLU 67": "OE1" <-> "OE2" Residue "t GLU 119": "OE1" <-> "OE2" Residue "u ASP 37": "OD1" <-> "OD2" Residue "u ASP 46": "OD1" <-> "OD2" Residue "u GLU 66": "OE1" <-> "OE2" Residue "u ASP 77": "OD1" <-> "OD2" Residue "u ASP 91": "OD1" <-> "OD2" Residue "u GLU 99": "OE1" <-> "OE2" Residue "u GLU 112": "OE1" <-> "OE2" Residue "u GLU 122": "OE1" <-> "OE2" Residue "u ASP 171": "OD1" <-> "OD2" Residue "u GLU 180": "OE1" <-> "OE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "v ASP 56": "OD1" <-> "OD2" Residue "v ASP 57": "OD1" <-> "OD2" Residue "v ASP 64": "OD1" <-> "OD2" Residue "w ASP 6": "OD1" <-> "OD2" Residue "y ASP 40": "OD1" <-> "OD2" Residue "z GLU 37": "OE1" <-> "OE2" Residue "z ASP 56": "OD1" <-> "OD2" Residue "0 GLU 54": "OE1" <-> "OE2" Residue "2 GLU 34": "OE1" <-> "OE2" Residue "4 ASP 36": "OD1" <-> "OD2" Residue "4 TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 144606 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 32340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1505, 32340 Classifications: {'RNA': 1505} Modifications used: {'rna2p': 2, 'rna2p_pur': 117, 'rna2p_pyr': 87, 'rna3p': 10, 'rna3p_pur': 727, 'rna3p_pyr': 562} Link IDs: {'rna2p': 205, 'rna3p': 1299} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1632 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 189} Chain: "E" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1309 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "F" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 785 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1021 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "K" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 858 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "L" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "O" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "Q" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 728 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "R" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 527 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "T" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 673 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 994 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "X" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 277 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1613 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 201} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1225 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "J" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1012 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "M" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "S" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 474 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "U" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 658 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "B" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1836 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "c" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2091 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 19, 'TRANS': 254} Chain: "d" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1586 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 204} Chain: "e" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain: "f" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1468 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "g" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1376 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "i" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1139 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 135} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1072 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "l" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1082 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "m" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "n" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "o" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 896 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "p" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 958 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "q" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 778 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "r" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "s" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "t" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Chain: "u" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1376 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "v" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 591 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "w" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 474 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "x" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 564 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "y" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 467 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 477 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "0" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 423 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "1" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 513 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "4" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 512 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" Number of atoms: 62531 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2903, 62406 Classifications: {'DNA': 1, 'RNA': 2902} Modifications used: {'rna2p': 4, 'rna2p_pur': 291, 'rna2p_pyr': 151, 'rna3p': 14, 'rna3p_pur': 1361, 'rna3p_pyr': 1072} Link IDs: {'rna2p': 446, 'rna3p': 2456} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 13 Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 2903, 62406 Classifications: {'DNA': 1, 'RNA': 2902} Modifications used: {'rna2p': 4, 'rna2p_pur': 291, 'rna2p_pyr': 151, 'rna3p': 14, 'rna3p_pur': 1361, 'rna3p_pyr': 1072} Link IDs: {'rna2p': 446, 'rna3p': 2456} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 13 Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 69720 Chain: "b" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2567 Classifications: {'DNA': 1, 'RNA': 119} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 61, 'rna3p_pyr': 49} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "V" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 183 Classifications: {'peptide': 23} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "Y" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 211 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 6} Chain: "C" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 65} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 117 Unusual residues: {' MG': 82, 'V7A': 1} Classifications: {'undetermined': 83} Link IDs: {None: 82} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" 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: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 329 Unusual residues: {' MG': 294, 'V7A': 1} Classifications: {'undetermined': 295} Link IDs: {None: 294} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 48591 SG CYS S 24 118.024 187.728 75.323 1.00 68.29 S ATOM 48617 SG CYS S 27 117.257 183.789 76.014 1.00 69.39 S ATOM 48723 SG CYS S 40 120.591 185.964 77.435 1.00 69.26 S ATOM 48748 SG CYS S 43 119.944 185.526 73.902 1.00 70.06 S ATOM 72828 SG CYS w 5 175.167 106.829 188.668 1.00 53.01 S ATOM 72850 SG CYS w 8 174.122 108.415 192.102 1.00 55.22 S ATOM 73199 SG CYS w 50 175.152 110.328 188.759 1.00 52.40 S ATOM 73218 SG CYS w 53 177.297 109.195 190.837 1.00 54.74 S ATOM 74548 SG CYS z 30 78.090 35.207 182.563 1.00 63.67 S ATOM 74579 SG CYS z 35 80.872 34.070 185.344 1.00 66.95 S ATOM 74654 SG CYS z 45 81.703 36.608 183.065 1.00 60.66 S ATOM 74673 SG CYS z 48 81.056 33.788 181.566 1.00 64.36 S ATOM 74863 SG CYS 0 16 146.163 169.060 198.383 1.00 82.24 S ATOM 74885 SG CYS 0 19 146.688 168.941 201.275 1.00 81.38 S ATOM 75095 SG CYS 0 43 143.801 169.686 201.176 1.00 72.09 S ATOM 75119 SG CYS 0 46 145.984 171.392 201.925 1.00 75.69 S ATOM 76214 SG CYS 4 16 121.633 222.312 149.194 1.00146.24 S ATOM 76227 SG CYS 4 18 120.696 224.455 148.271 1.00148.85 S ATOM 76369 SG CYS 4 38 118.836 223.038 149.006 1.00145.44 S ATOM 76390 SG CYS 4 41 119.432 223.683 145.564 1.00146.02 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" P A G a2244 " occ=0.41 ... (44 atoms not shown) pdb=" C4 B G a2244 " occ=0.59 residue: pdb=" P A A a2245 " occ=0.41 ... (42 atoms not shown) pdb=" C4 B A a2245 " occ=0.59 residue: pdb=" P A C a2246 " occ=0.41 ... (38 atoms not shown) pdb=" C6 B C a2246 " occ=0.59 residue: pdb=" P A U a2791 " occ=0.45 ... (38 atoms not shown) pdb=" C6 B U a2791 " occ=0.55 residue: pdb=" P A C a2792 " occ=0.45 ... (38 atoms not shown) pdb=" C6 B C a2792 " occ=0.55 residue: pdb=" P A C a2793 " occ=0.45 ... (38 atoms not shown) pdb=" C6 B C a2793 " occ=0.55 Time building chain proxies: 78.11, per 1000 atoms: 0.54 Number of scatterers: 144606 At special positions: 0 Unit cell: (237.096, 249.912, 280.884, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 156 16.00 P 4620 15.00 Mg 386 11.99 O 40551 8.00 N 26779 7.00 C 72109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 3 11 " - pdb=" SG CYS 3 14 " distance=2.48 Simple disulfide: pdb=" SG CYS 3 11 " - pdb=" SG CYS 3 27 " distance=3.00 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: 65.74 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 101 " pdb="ZN ZN 0 101 " - pdb=" SG CYS 0 46 " pdb="ZN ZN 0 101 " - pdb=" SG CYS 0 16 " pdb="ZN ZN 0 101 " - pdb=" SG CYS 0 43 " pdb="ZN ZN 0 101 " - pdb=" SG CYS 0 19 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 38 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 41 " pdb=" ZN S 101 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 43 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 40 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 24 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 27 " pdb=" ZN w 101 " pdb="ZN ZN w 101 " - pdb=" SG CYS w 5 " pdb="ZN ZN w 101 " - pdb=" SG CYS w 53 " pdb="ZN ZN w 101 " - pdb=" SG CYS w 50 " pdb="ZN ZN w 101 " - pdb=" SG CYS w 8 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 30 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 48 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 35 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 45 " Number of angles added : 30 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10462 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... Warning! N3 atom is missing from residue C a 127 Was trying to link: C a 127 N3 with G a 122 N1, Saenger class: 19 Warning! N3 atom is missing from residue C a 127 Was trying to link: C a 127 N3 with G a 122 N2, Saenger class: 22 Warning! N3 atom is missing from residue C a 127 Was trying to link: C a 127 N3 with G a 122 N1, Saenger class: 19 Warning! N3 atom is missing from residue C a 127 Was trying to link: C a 127 N3 with G a 122 N2, Saenger class: 22 Warning! O6 atom is missing from residue G a2872 Was trying to link: G a2872 O6 with G a3052 N1, Saenger class: 6 Warning! O6 atom is missing from residue G a2872 Was trying to link: G a2872 O6 with G a3052 N2, Saenger class: 7 Warning! O6 atom is missing from residue G a1837 Was trying to link: G a1837 O6 with G a3002 N1, Saenger class: 6 Warning! O6 atom is missing from residue G a1837 Was trying to link: G a1837 O6 with G a3002 N2, Saenger class: 7 Secondary structure from input PDB file: 171 helices and 71 sheets defined 37.8% alpha, 18.9% beta 1422 base pairs and 2551 stacking pairs defined. Time for finding SS restraints: 78.71 Creating SS restraints... Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.235A pdb=" N LYS D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 removed outlier: 4.975A pdb=" N ARG D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) Proline residue: D 30 - end of helix No H-bonds generated for 'chain 'D' and resid 25 through 30' Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 63 through 78 removed outlier: 5.073A pdb=" N GLN D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 93 removed outlier: 5.960A pdb=" N LEU D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 Processing helix chain 'D' and resid 105 through 116 Processing helix chain 'D' and resid 147 through 161 removed outlier: 5.698A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP D 161 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 removed outlier: 5.183A pdb=" N VAL D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.610A pdb=" N SER D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 94 removed outlier: 4.174A pdb=" N LYS E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N HIS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 155 through 171 removed outlier: 3.664A pdb=" N LEU E 170 " --> pdb=" O ALA E 166 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLU E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 181 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 189 through 210 Processing helix chain 'F' and resid 15 through 32 removed outlier: 5.876A pdb=" N VAL F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 83 removed outlier: 5.477A pdb=" N GLU F 83 " --> pdb=" O LEU F 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 117 through 125 Processing helix chain 'K' and resid 52 through 57 removed outlier: 3.965A pdb=" N GLY K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.521A pdb=" N SER K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR K 65 " --> pdb=" O SER K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 65' Processing helix chain 'K' and resid 66 through 84 Processing helix chain 'K' and resid 98 through 110 Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.759A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 14 removed outlier: 6.396A pdb=" N LYS O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 45 Processing helix chain 'O' and resid 47 through 72 Processing helix chain 'O' and resid 73 through 84 removed outlier: 3.591A pdb=" N GLY O 84 " --> pdb=" O ILE O 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 14 removed outlier: 5.355A pdb=" N ILE R 13 " --> pdb=" O LYS R 9 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS R 14 " --> pdb=" O VAL R 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 9 through 14' Processing helix chain 'R' and resid 25 through 33 removed outlier: 3.957A pdb=" N LEU R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'T' and resid 4 through 42 Processing helix chain 'T' and resid 44 through 65 Processing helix chain 'T' and resid 68 through 88 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 78 Processing helix chain 'P' and resid 79 through 84 removed outlier: 4.638A pdb=" N THR P 84 " --> pdb=" O TRP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 112 removed outlier: 4.963A pdb=" N LEU P 104 " --> pdb=" O ASN P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 129 Processing helix chain 'X' and resid 3 through 31 removed outlier: 6.531A pdb=" N LYS X 7 " --> pdb=" O SER X 3 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE X 26 " --> pdb=" O LYS X 22 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN X 27 " --> pdb=" O ARG X 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 12 Processing helix chain 'G' and resid 27 through 46 Processing helix chain 'G' and resid 71 through 77 removed outlier: 4.623A pdb=" N VAL G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 95 Processing helix chain 'G' and resid 107 through 112 removed outlier: 5.445A pdb=" N ALA G 112 " --> pdb=" O PRO G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 126 Processing helix chain 'G' and resid 128 through 144 Processing helix chain 'I' and resid 20 through 31 removed outlier: 3.741A pdb=" N SER I 24 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 55 removed outlier: 4.287A pdb=" N ASN I 55 " --> pdb=" O ARG I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 70 Processing helix chain 'I' and resid 92 through 111 Processing helix chain 'I' and resid 115 through 130 Processing helix chain 'I' and resid 132 through 149 Processing helix chain 'J' and resid 76 through 82 Proline residue: J 82 - end of helix Processing helix chain 'J' and resid 83 through 98 removed outlier: 3.950A pdb=" N GLN J 87 " --> pdb=" O ASN J 83 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE J 89 " --> pdb=" O VAL J 85 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL J 90 " --> pdb=" O HIS J 86 " (cutoff:3.500A) Proline residue: J 93 - end of helix removed outlier: 4.486A pdb=" N GLY J 98 " --> pdb=" O PHE J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 134 Proline residue: J 134 - end of helix Processing helix chain 'J' and resid 137 through 145 removed outlier: 4.047A pdb=" N GLY J 145 " --> pdb=" O LEU J 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 33 Processing helix chain 'M' and resid 80 through 90 Processing helix chain 'N' and resid 14 through 22 removed outlier: 4.036A pdb=" N THR N 20 " --> pdb=" O GLU N 16 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 38 Processing helix chain 'N' and resid 49 through 64 Processing helix chain 'N' and resid 67 through 85 Processing helix chain 'N' and resid 86 through 95 Processing helix chain 'N' and resid 107 through 112 Processing helix chain 'S' and resid 3 through 13 removed outlier: 5.253A pdb=" N LYS S 13 " --> pdb=" O LYS S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 51 Processing helix chain 'U' and resid 12 through 26 removed outlier: 5.874A pdb=" N ALA U 16 " --> pdb=" O ASP U 12 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 76 removed outlier: 4.465A pdb=" N PHE U 74 " --> pdb=" O LYS U 70 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA U 75 " --> pdb=" O LEU U 71 " (cutoff:3.500A) Proline residue: U 76 - end of helix No H-bonds generated for 'chain 'U' and resid 70 through 76' Processing helix chain 'U' and resid 64 through 69 removed outlier: 3.727A pdb=" N VAL U 67 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY U 68 " --> pdb=" O SER U 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 13 removed outlier: 4.576A pdb=" N LEU B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 64 removed outlier: 4.230A pdb=" N LEU B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR B 48 " --> pdb=" O HIS B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 removed outlier: 4.798A pdb=" N GLU B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER B 79 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 127 removed outlier: 3.904A pdb=" N ALA B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 149 removed outlier: 5.925A pdb=" N LEU B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N MET B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.155A pdb=" N VAL B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASP B 198 " --> pdb=" O PRO B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 193 through 198' Processing helix chain 'B' and resid 209 through 233 removed outlier: 4.317A pdb=" N LEU B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.814A pdb=" N ARG B 153 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET B 155 " --> pdb=" O ILE B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 155' Processing helix chain 'c' and resid 11 through 16 removed outlier: 7.754A pdb=" N GLY c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 11 through 16' Processing helix chain 'c' and resid 132 through 137 Proline residue: c 137 - end of helix Processing helix chain 'c' and resid 208 through 216 removed outlier: 3.751A pdb=" N ASN c 212 " --> pdb=" O LYS c 208 " (cutoff:3.500A) Processing helix chain 'c' and resid 222 through 227 removed outlier: 4.202A pdb=" N MET c 226 " --> pdb=" O ARG c 222 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN c 227 " --> pdb=" O GLY c 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 222 through 227' Processing helix chain 'c' and resid 263 through 268 removed outlier: 4.104A pdb=" N LEU c 267 " --> pdb=" O ALA c 263 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE c 268 " --> pdb=" O SER c 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 263 through 268' Processing helix chain 'd' and resid 62 through 67 removed outlier: 3.562A pdb=" N VAL d 66 " --> pdb=" O LYS d 62 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR d 67 " --> pdb=" O ALA d 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 62 through 67' Processing helix chain 'd' and resid 68 through 78 Processing helix chain 'd' and resid 92 through 97 removed outlier: 4.099A pdb=" N TYR d 96 " --> pdb=" O ASP d 92 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR d 97 " --> pdb=" O ALA d 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 92 through 97' Processing helix chain 'd' and resid 126 through 131 Processing helix chain 'd' and resid 103 through 108 removed outlier: 4.872A pdb=" N SER d 108 " --> pdb=" O ASP d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 50 Processing helix chain 'e' and resid 23 through 28 removed outlier: 6.835A pdb=" N PHE e 27 " --> pdb=" O PRO e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 49 removed outlier: 5.501A pdb=" N GLN e 49 " --> pdb=" O ALA e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 61 removed outlier: 6.133A pdb=" N SER e 61 " --> pdb=" O ARG e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 124 removed outlier: 3.845A pdb=" N MET e 120 " --> pdb=" O ALA e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 150 removed outlier: 4.325A pdb=" N GLN e 142 " --> pdb=" O PRO e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 164 through 173 removed outlier: 4.796A pdb=" N ASN e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) Processing helix chain 'e' and resid 186 through 194 removed outlier: 5.372A pdb=" N ARG e 194 " --> pdb=" O VAL e 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 199 through 211 Processing helix chain 'f' and resid 11 through 29 Processing helix chain 'f' and resid 51 through 56 removed outlier: 5.195A pdb=" N ASP f 55 " --> pdb=" O ASP f 51 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N SER f 56 " --> pdb=" O ALA f 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 51 through 56' Processing helix chain 'f' and resid 57 through 71 Processing helix chain 'f' and resid 102 through 121 removed outlier: 5.297A pdb=" N LEU f 117 " --> pdb=" O LEU f 113 " (cutoff:3.500A) Proline residue: f 118 - end of helix removed outlier: 6.163A pdb=" N ARG f 121 " --> pdb=" O LEU f 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 171 through 183 Processing helix chain 'f' and resid 143 through 148 removed outlier: 4.880A pdb=" N MET f 146 " --> pdb=" O GLU f 143 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU f 148 " --> pdb=" O VAL f 145 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 8 removed outlier: 3.753A pdb=" N LEU g 7 " --> pdb=" O ARG g 3 " (cutoff:3.500A) Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 59 through 82 removed outlier: 3.679A pdb=" N ARG g 63 " --> pdb=" O GLU g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 139 through 155 removed outlier: 4.029A pdb=" N ARG g 154 " --> pdb=" O ILE g 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 38 Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 3.728A pdb=" N LYS i 120 " --> pdb=" O ARG i 116 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS i 121 " --> pdb=" O GLN i 117 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU i 122 " --> pdb=" O GLN i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 108 removed outlier: 4.557A pdb=" N ARG j 107 " --> pdb=" O ALA j 103 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU 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 38 through 43 removed outlier: 3.928A pdb=" N ARG k 42 " --> pdb=" O GLY k 38 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 60 Processing helix chain 'k' and resid 78 through 87 Proline residue: k 87 - end of helix Processing helix chain 'k' and resid 94 through 102 Processing helix chain 'k' and resid 129 through 140 Processing helix chain 'l' and resid 43 through 59 Processing helix chain 'l' and resid 110 through 126 removed outlier: 3.920A pdb=" N LYS l 124 " --> pdb=" O LEU l 120 " (cutoff:3.500A) removed outlier: 3.687A 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 56 Proline residue: m 46 - end of helix Processing helix chain 'm' and resid 59 through 71 removed outlier: 3.979A pdb=" N THR m 69 " --> pdb=" O PHE m 65 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE m 70 " --> pdb=" O VAL m 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR m 71 " --> pdb=" O ASN m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 3.729A pdb=" N ILE m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix removed outlier: 4.016A pdb=" N GLU m 88 " --> pdb=" O GLY m 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 29 removed outlier: 4.285A pdb=" N LYS n 28 " --> pdb=" O ARG n 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 74 removed outlier: 4.434A pdb=" N GLU n 72 " --> pdb=" O ALA n 68 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET n 73 " --> pdb=" O GLU n 69 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N SER n 74 " --> pdb=" O LEU n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 76 through 96 Processing helix chain 'n' and resid 111 through 124 Processing helix chain 'o' and resid 2 through 13 removed outlier: 3.577A pdb=" N ASP o 6 " --> pdb=" O SER o 2 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA o 11 " --> pdb=" O GLU o 7 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER o 12 " --> pdb=" O ILE o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.607A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ARG o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 8 through 22 removed outlier: 4.508A pdb=" N LYS p 12 " --> pdb=" O VAL p 8 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS p 13 " --> pdb=" O ASN p 9 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG p 14 " --> pdb=" O ALA p 10 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.942A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 72 removed outlier: 3.568A pdb=" N ARG p 51 " --> pdb=" O PHE p 47 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN p 72 " --> pdb=" O ALA p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 101 removed outlier: 6.184A pdb=" N ALA p 96 " --> pdb=" O ARG p 92 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 117 Processing helix chain 'q' and resid 49 through 57 removed outlier: 3.795A pdb=" N LYS q 55 " --> pdb=" O ASP q 51 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL q 56 " --> pdb=" O ALA q 52 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LYS q 57 " --> pdb=" O LEU q 53 " (cutoff:3.500A) Processing helix chain 'r' and resid 8 through 14 Processing helix chain 'r' and resid 30 through 42 removed outlier: 4.171A pdb=" N VAL r 37 " --> pdb=" O LYS r 33 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU r 40 " --> pdb=" O ARG r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 56 removed outlier: 3.794A pdb=" N PHE r 55 " --> pdb=" O THR r 51 " (cutoff:3.500A) Processing helix chain 'r' and resid 58 through 79 removed outlier: 4.694A pdb=" N GLU r 62 " --> pdb=" O GLN r 58 " (cutoff:3.500A) Proline residue: r 63 - end of helix Processing helix chain 'r' and resid 126 through 132 removed outlier: 4.202A pdb=" N ARG r 130 " --> pdb=" O PRO r 126 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN r 131 " --> pdb=" O LYS r 127 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA r 132 " --> pdb=" O GLU r 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 126 through 132' Processing helix chain 's' and resid 8 through 14 removed outlier: 4.274A pdb=" N ILE s 12 " --> pdb=" O ASP s 8 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE s 13 " --> pdb=" O PRO s 9 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU s 14 " --> pdb=" O ARG s 10 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 8 through 14' Processing helix chain 's' and resid 19 through 29 removed outlier: 3.889A pdb=" N ASP s 27 " --> pdb=" O TYR s 23 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN s 28 " --> pdb=" O GLY s 24 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN s 29 " --> pdb=" O LEU s 25 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 53 Processing helix chain 't' and resid 71 through 76 removed outlier: 4.100A pdb=" N VAL t 75 " --> pdb=" O HIS t 71 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLN t 76 " --> pdb=" O VAL t 72 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 71 through 76' Processing helix chain 'u' and resid 16 through 27 Processing helix chain 'u' and resid 46 through 55 Processing helix chain 'w' and resid 50 through 57 Processing helix chain 'x' and resid 7 through 13 removed outlier: 4.683A pdb=" N GLN x 11 " --> pdb=" O ALA x 7 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU x 12 " --> pdb=" O GLU x 8 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER x 13 " --> pdb=" O LEU x 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 7 through 13' Processing helix chain 'x' and resid 14 through 38 Processing helix chain 'x' and resid 42 through 66 removed outlier: 4.486A pdb=" N LEU x 46 " --> pdb=" O ASN x 42 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG x 47 " --> pdb=" O THR x 43 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG x 50 " --> pdb=" O LEU x 46 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 21 removed outlier: 4.209A pdb=" N GLN z 19 " --> pdb=" O HIS z 15 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TRP z 20 " --> pdb=" O ARG z 16 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS z 21 " --> pdb=" O ARG z 17 " (cutoff:3.500A) Processing helix chain '0' and resid 29 through 34 Proline residue: 0 34 - end of helix No H-bonds generated for 'chain '0' and resid 29 through 34' Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.072A pdb=" N THR 1 24 " --> pdb=" O SER 1 20 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG 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 32 through 37 removed outlier: 4.634A pdb=" N LYS 2 36 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N SER 2 37 " --> pdb=" O ASN 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 removed outlier: 4.245A pdb=" N GLY 2 46 " --> pdb=" O ARG 2 42 " (cutoff:3.500A) Processing helix chain '2' and resid 51 through 63 removed outlier: 4.875A pdb=" N ALA 2 63 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '4' and resid 42 through 47 removed outlier: 3.792A pdb=" N THR 4 46 " --> pdb=" O HIS 4 42 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY 4 47 " --> pdb=" O PRO 4 43 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 42 through 47' Processing helix chain '4' and resid 56 through 66 Processing helix chain 'V' and resid 2 through 12 removed outlier: 4.398A pdb=" N ARG V 12 " --> pdb=" O ARG V 8 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'D' and resid 136 through 140 removed outlier: 4.067A pdb=" N ASP D 136 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY D 173 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG D 174 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.795A pdb=" N LEU E 59 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'E' and resid 107 through 111 removed outlier: 3.584A pdb=" N ALA E 122 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASP E 145 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 56 through 64 removed outlier: 6.795A pdb=" N SER E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'F' and resid 39 through 43 removed outlier: 6.176A pdb=" N TYR F 60 " --> pdb=" O TRP F 43 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'F' and resid 44 through 48 removed outlier: 3.681A pdb=" N GLY F 44 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N SER F 56 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.323A pdb=" N ASP H 23 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LYS H 61 " --> pdb=" O HIS H 29 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'H' and resid 79 through 82 removed outlier: 4.181A pdb=" N ARG H 81 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE H 108 " --> pdb=" O LEU H 131 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'K' and resid 48 through 51 removed outlier: 4.745A pdb=" N GLY K 25 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP K 89 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL K 90 " --> pdb=" O PRO K 115 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL K 92 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLY K 94 " --> pdb=" O VAL K 119 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.136A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'L' and resid 35 through 41 removed outlier: 5.199A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'Q' and resid 13 through 18 removed outlier: 5.504A pdb=" N LYS Q 13 " --> pdb=" O GLU Q 70 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG Q 67 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Q' and resid 26 through 37 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'P' and resid 5 through 11 Processing sheet with id= 15, first strand: chain 'G' and resid 53 through 58 removed outlier: 3.504A pdb=" N SER G 53 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL G 105 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 163 through 169 removed outlier: 3.731A pdb=" N GLY G 147 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY G 193 " --> pdb=" O THR G 190 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP G 180 " --> pdb=" O LYS G 203 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 72 through 79 removed outlier: 6.173A pdb=" N SER I 72 " --> pdb=" O VAL I 91 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'J' and resid 47 through 51 Processing sheet with id= 19, first strand: chain 'M' and resid 39 through 42 removed outlier: 4.692A pdb=" N LYS M 71 " --> pdb=" O LEU M 42 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE M 6 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG M 11 " --> pdb=" O ASP M 97 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'M' and resid 44 through 52 removed outlier: 3.617A pdb=" N ASN M 47 " --> pdb=" O MET M 67 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'U' and resid 30 through 34 removed outlier: 4.109A pdb=" N HIS U 47 " --> pdb=" O VAL U 62 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.218A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.595A pdb=" N VAL B 165 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'c' and resid 33 through 36 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'c' and resid 74 through 79 removed outlier: 4.943A pdb=" N VAL c 75 " --> pdb=" O SER c 119 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER c 119 " --> pdb=" O VAL c 75 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR c 115 " --> pdb=" O VAL c 79 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLY c 128 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL c 118 " --> pdb=" O GLY c 128 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'c' and resid 81 through 84 removed outlier: 5.443A pdb=" N ARG c 91 " --> pdb=" O ALA c 107 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'c' and resid 139 through 143 removed outlier: 3.661A pdb=" N THR c 140 " --> pdb=" O LEU c 165 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR c 174 " --> pdb=" O VAL c 166 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU c 181 " --> pdb=" O LEU c 177 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'd' and resid 8 through 12 removed outlier: 6.034A pdb=" N LYS d 8 " --> pdb=" O SER d 211 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU d 174 " --> pdb=" O SER d 119 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'd' and resid 16 through 22 removed outlier: 3.716A pdb=" N GLY d 16 " --> pdb=" O VAL d 32 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG d 26 " --> pdb=" O ASP d 22 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 38 through 41 removed outlier: 5.936A pdb=" N VAL d 39 " --> pdb=" O GLY d 57 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLN d 55 " --> pdb=" O THR d 41 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR d 58 " --> pdb=" O HIS d 84 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'd' and resid 111 through 114 removed outlier: 4.678A pdb=" N ASP d 111 " --> pdb=" O VAL d 183 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 125 through 128 removed outlier: 3.560A pdb=" N THR e 195 " --> pdb=" O LEU e 153 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'f' and resid 74 through 77 removed outlier: 3.779A pdb=" N GLY f 95 " --> pdb=" O THR f 77 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE f 94 " --> pdb=" O VAL f 49 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY f 48 " --> pdb=" O GLY f 160 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY f 160 " --> pdb=" O GLY f 48 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'g' and resid 16 through 19 Processing sheet with id= 35, first strand: chain 'g' and resid 41 through 46 removed outlier: 4.653A pdb=" N ASN g 46 " --> pdb=" O ALA g 50 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA g 50 " --> pdb=" O ASN g 46 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'g' and resid 83 through 90 removed outlier: 5.559A pdb=" N THR g 131 " --> pdb=" O ILE g 90 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'g' and resid 95 through 100 removed outlier: 5.189A pdb=" N GLN g 104 " --> pdb=" O LYS g 100 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS g 103 " --> pdb=" O ALA g 119 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'i' and resid 52 through 57 removed outlier: 5.006A pdb=" N ASP i 19 " --> pdb=" O TYR i 140 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.446A pdb=" N GLY i 83 " --> pdb=" O SER i 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.475A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASN j 82 " --> pdb=" O ARG j 7 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU j 86 " --> pdb=" O ALA j 11 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYS j 59 " --> pdb=" O LEU j 87 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP j 37 " --> pdb=" O VAL j 62 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'j' and resid 68 through 71 removed outlier: 3.922A pdb=" N SER j 75 " --> pdb=" O ARG j 71 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 63 through 66 removed outlier: 4.851A pdb=" N ARG j 64 " --> pdb=" O ALA j 83 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL j 66 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU j 81 " --> pdb=" O VAL j 66 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'k' and resid 74 through 77 Processing sheet with id= 44, first strand: chain 'k' and resid 121 through 124 removed outlier: 6.093A pdb=" N THR k 144 " --> pdb=" O LEU k 123 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 38 through 41 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'l' and resid 63 through 66 removed outlier: 3.816A pdb=" N PHE l 104 " --> pdb=" O ILE l 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE l 34 " --> pdb=" O LEU l 103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG l 101 " --> pdb=" O ALA l 36 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 32 through 37 removed outlier: 6.530A pdb=" N LYS l 128 " --> pdb=" O THR l 37 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.798A pdb=" N ALA m 111 " --> pdb=" O THR m 36 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA m 108 " --> pdb=" O ILE m 102 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE m 102 " --> pdb=" O ALA m 108 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET m 110 " --> pdb=" O ILE m 100 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'n' and resid 37 through 42 removed outlier: 3.719A pdb=" N VAL n 61 " --> pdb=" O VAL n 51 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.389A pdb=" N SER o 25 " --> pdb=" O ASP o 87 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS o 83 " --> pdb=" O HIS o 29 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.794A pdb=" N SER o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY o 53 " --> pdb=" O GLN o 56 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'q' and resid 11 through 15 removed outlier: 5.217A pdb=" N SER q 45 " --> pdb=" O ASP q 42 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'q' and resid 18 through 21 removed outlier: 4.249A pdb=" N ASP q 18 " --> pdb=" O VAL q 97 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL q 58 " --> pdb=" O LEU q 35 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER q 31 " --> pdb=" O VAL q 62 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 70 through 77 removed outlier: 3.567A pdb=" N LYS q 77 " --> pdb=" O TYR q 82 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR q 82 " --> pdb=" O LYS q 77 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'r' and resid 19 through 25 removed outlier: 4.830A pdb=" N SER r 117 " --> pdb=" O GLY r 96 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'r' and resid 97 through 105 removed outlier: 4.803A pdb=" N ILE r 97 " --> pdb=" O SER r 117 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER r 117 " --> pdb=" O ILE r 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER r 109 " --> pdb=" O ARG r 105 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 's' and resid 30 through 35 removed outlier: 4.448A pdb=" N LYS s 82 " --> pdb=" O VAL s 35 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS s 67 " --> pdb=" O ARG s 78 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP s 80 " --> pdb=" O LYS s 65 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LYS s 65 " --> pdb=" O ASP s 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS s 82 " --> pdb=" O ASN s 63 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN s 63 " --> pdb=" O LYS s 82 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA s 84 " --> pdb=" O THR s 61 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR s 61 " --> pdb=" O ALA s 84 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL s 86 " --> pdb=" O VAL s 59 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL s 59 " --> pdb=" O VAL s 86 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 't' and resid 42 through 46 removed outlier: 4.969A pdb=" N ASN t 42 " --> pdb=" O ALA t 68 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE t 64 " --> pdb=" O HIS t 46 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 't' and resid 89 through 95 removed outlier: 5.205A pdb=" N ARG t 89 " --> pdb=" O LYS t 117 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'u' and resid 4 through 9 removed outlier: 4.844A pdb=" N LEU u 72 " --> pdb=" O VAL u 95 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP u 91 " --> pdb=" O LYS u 76 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'u' and resid 138 through 144 removed outlier: 3.523A pdb=" N ARG u 108 " --> pdb=" O ILE u 139 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE u 141 " --> pdb=" O ARG u 108 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL u 143 " --> pdb=" O THR u 110 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU u 127 " --> pdb=" O LEU u 166 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'u' and resid 149 through 152 removed outlier: 3.739A pdb=" N THR u 150 " --> pdb=" O VAL u 176 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'u' and resid 77 through 80 removed outlier: 3.726A pdb=" N ASP u 77 " --> pdb=" O ASP u 91 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 37 through 40 removed outlier: 4.434A pdb=" N GLN v 40 " --> pdb=" O ASP v 57 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP v 57 " --> pdb=" O GLN v 40 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'v' and resid 66 through 70 Processing sheet with id= 66, first strand: chain 'w' and resid 12 through 18 Processing sheet with id= 67, first strand: chain 'z' and resid 49 through 52 removed outlier: 7.854A pdb=" N GLY z 49 " --> pdb=" O VAL z 60 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '0' and resid 23 through 27 removed outlier: 5.804A pdb=" N THR 0 13 " --> pdb=" O THR 0 55 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '2' and resid 22 through 25 removed outlier: 5.963A pdb=" N VAL 2 22 " --> pdb=" O LEU 2 50 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '4' and resid 20 through 24 removed outlier: 6.016A pdb=" N ASN 4 20 " --> pdb=" O CYS 4 16 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '3' and resid 14 through 19 1883 hydrogen bonds defined for protein. 5553 hydrogen bond angles defined for protein. NA hbond rejected because one of the atoms is absent Restraints generated for nucleic acids: 3566 hydrogen bonds 5394 hydrogen bond angles 0 basepair planarities 1422 basepair parallelities 2554 stacking parallelities Total time for adding SS restraints: 277.92 Time building geometry restraints manager: 70.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12823 1.30 - 1.43: 69864 1.43 - 1.56: 64395 1.56 - 1.69: 9237 1.69 - 1.81: 272 Bond restraints: 156591 Sorted by residual: bond pdb=" CAI V7A A1601 " pdb=" CAL V7A A1601 " ideal model delta sigma weight residual 0.000 1.362 -1.362 2.00e-02 2.50e+03 4.64e+03 bond pdb=" CAI V7A a3101 " pdb=" CAL V7A a3101 " ideal model delta sigma weight residual 0.000 1.357 -1.357 2.00e-02 2.50e+03 4.60e+03 bond pdb=" CAH V7A A1601 " pdb=" CAI V7A A1601 " ideal model delta sigma weight residual 0.401 1.448 -1.047 2.00e-02 2.50e+03 2.74e+03 bond pdb=" CAH V7A a3101 " pdb=" CAI V7A a3101 " ideal model delta sigma weight residual 0.401 1.445 -1.044 2.00e-02 2.50e+03 2.73e+03 bond pdb=" CAI V7A A1601 " pdb=" CAJ V7A A1601 " ideal model delta sigma weight residual 2.379 1.508 0.871 2.00e-02 2.50e+03 1.90e+03 ... (remaining 156586 not shown) Histogram of bond angle deviations from ideal: 96.39 - 105.87: 24847 105.87 - 115.35: 108168 115.35 - 124.83: 81739 124.83 - 134.32: 19700 134.32 - 143.80: 4 Bond angle restraints: 234458 Sorted by residual: angle pdb=" CAD V7A A1601 " pdb=" CAE V7A A1601 " pdb=" CAH V7A A1601 " ideal model delta sigma weight residual 39.59 119.93 -80.34 3.00e+00 1.11e-01 7.17e+02 angle pdb=" CAD V7A a3101 " pdb=" CAE V7A a3101 " pdb=" CAH V7A a3101 " ideal model delta sigma weight residual 39.59 119.83 -80.24 3.00e+00 1.11e-01 7.15e+02 angle pdb=" CAH V7A A1601 " pdb=" CAI V7A A1601 " pdb=" CAJ V7A A1601 " ideal model delta sigma weight residual 169.27 114.71 54.56 3.00e+00 1.11e-01 3.31e+02 angle pdb=" CAH V7A a3101 " pdb=" CAI V7A a3101 " pdb=" CAJ V7A a3101 " ideal model delta sigma weight residual 169.27 119.49 49.78 3.00e+00 1.11e-01 2.75e+02 angle pdb=" CAE V7A a3101 " pdb=" CAH V7A a3101 " pdb=" CAI V7A a3101 " ideal model delta sigma weight residual 73.96 119.54 -45.58 3.00e+00 1.11e-01 2.31e+02 ... (remaining 234453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 88445 35.95 - 71.91: 11441 71.91 - 107.86: 1257 107.86 - 143.81: 31 143.81 - 179.77: 47 Dihedral angle restraints: 101221 sinusoidal: 84939 harmonic: 16282 Sorted by residual: dihedral pdb=" O4' U A 330 " pdb=" C1' U A 330 " pdb=" N1 U A 330 " pdb=" C2 U A 330 " ideal model delta sinusoidal sigma weight residual -160.00 15.99 -175.99 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U a 675 " pdb=" C1' U a 675 " pdb=" N1 U a 675 " pdb=" C2 U a 675 " ideal model delta sinusoidal sigma weight residual 200.00 25.31 174.69 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C a1623 " pdb=" C1' C a1623 " pdb=" N1 C a1623 " pdb=" C2 C a1623 " ideal model delta sinusoidal sigma weight residual 200.00 28.37 171.63 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 101218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.858: 29800 0.858 - 1.716: 0 1.716 - 2.574: 0 2.574 - 3.433: 0 3.433 - 4.291: 2 Chirality restraints: 29802 Sorted by residual: chirality pdb=" CAM V7A a3101 " pdb=" CAL V7A a3101 " pdb=" CAN V7A a3101 " pdb=" CAP V7A a3101 " both_signs ideal model delta sigma weight residual False 1.75 -2.54 4.29 2.00e-01 2.50e+01 4.60e+02 chirality pdb=" CAM V7A A1601 " pdb=" CAL V7A A1601 " pdb=" CAN V7A A1601 " pdb=" CAP V7A A1601 " both_signs ideal model delta sigma weight residual False 1.75 -2.40 4.15 2.00e-01 2.50e+01 4.31e+02 chirality pdb=" C1' U a2961 " pdb=" O4' U a2961 " pdb=" C2' U a2961 " pdb=" N1 U a2961 " both_signs ideal model delta sigma weight residual False 2.46 1.74 0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 29799 not shown) Planarity restraints: 12568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a2627 " 0.050 2.00e-02 2.50e+03 6.00e-01 8.10e+03 pdb=" C4' 2MG a2627 " 0.446 2.00e-02 2.50e+03 pdb=" O4' 2MG a2627 " 0.697 2.00e-02 2.50e+03 pdb=" C3' 2MG a2627 " -0.598 2.00e-02 2.50e+03 pdb=" O3' 2MG a2627 " -0.607 2.00e-02 2.50e+03 pdb=" C2' 2MG a2627 " -0.205 2.00e-02 2.50e+03 pdb=" O2' 2MG a2627 " 0.936 2.00e-02 2.50e+03 pdb=" C1' 2MG a2627 " 0.209 2.00e-02 2.50e+03 pdb=" N9 2MG a2627 " -0.929 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1503 " 0.063 2.00e-02 2.50e+03 5.99e-01 8.08e+03 pdb=" C4' 2MG A1503 " 0.438 2.00e-02 2.50e+03 pdb=" O4' 2MG A1503 " 0.620 2.00e-02 2.50e+03 pdb=" C3' 2MG A1503 " -0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG A1503 " -0.642 2.00e-02 2.50e+03 pdb=" C2' 2MG A1503 " -0.173 2.00e-02 2.50e+03 pdb=" O2' 2MG A1503 " 0.982 2.00e-02 2.50e+03 pdb=" C1' 2MG A1503 " 0.223 2.00e-02 2.50e+03 pdb=" N9 2MG A1503 " -0.917 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1394 " 0.046 2.00e-02 2.50e+03 5.78e-01 7.52e+03 pdb=" C4' 5MC A1394 " 0.435 2.00e-02 2.50e+03 pdb=" O4' 5MC A1394 " 0.611 2.00e-02 2.50e+03 pdb=" C3' 5MC A1394 " -0.591 2.00e-02 2.50e+03 pdb=" O3' 5MC A1394 " -0.599 2.00e-02 2.50e+03 pdb=" C2' 5MC A1394 " -0.195 2.00e-02 2.50e+03 pdb=" O2' 5MC A1394 " 0.939 2.00e-02 2.50e+03 pdb=" C1' 5MC A1394 " 0.228 2.00e-02 2.50e+03 pdb=" N1 5MC A1394 " -0.874 2.00e-02 2.50e+03 ... (remaining 12565 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 778 2.38 - 3.01: 74436 3.01 - 3.64: 265433 3.64 - 4.27: 440572 4.27 - 4.90: 589288 Nonbonded interactions: 1370507 Sorted by model distance: nonbonded pdb=" OP1 C a1045 " pdb="MG MG a3138 " model vdw 1.748 2.170 nonbonded pdb=" OP2 U a2613 " pdb="MG MG a3222 " model vdw 1.770 2.170 nonbonded pdb=" O6 G a2672 " pdb="MG MG a3116 " model vdw 1.793 2.170 nonbonded pdb="MG MG b 201 " pdb=" O HOH b 301 " model vdw 1.824 2.170 nonbonded pdb=" OP2 U a2864 " pdb="MG MG a3327 " model vdw 1.833 2.170 ... (remaining 1370502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 14.050 Check model and map are aligned: 1.540 Set scattering table: 0.960 Process input model: 629.910 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 663.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 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 : 0.012 1.362 156591 Z= 0.650 Angle : 0.763 80.341 234458 Z= 0.380 Chirality : 0.056 4.291 29802 Planarity : 0.019 0.600 12568 Dihedral : 23.626 179.765 90753 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.80 % Allowed : 5.74 % Favored : 93.46 % Rotamer: Outliers : 1.38 % Allowed : 0.81 % Favored : 97.81 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.41 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 5646 helix: 1.03 (0.12), residues: 1867 sheet: -0.32 (0.15), residues: 1050 loop : -0.86 (0.12), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.002 TRP c 214 HIS 0.007 0.001 HIS E 161 PHE 0.032 0.002 PHE f 184 TYR 0.024 0.002 TYR N 64 ARG 0.009 0.000 ARG w 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1554 time to evaluate : 5.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 66 GLN cc_start: 0.7734 (tt0) cc_final: 0.7471 (tt0) REVERT: D 171 ASN cc_start: 0.7141 (OUTLIER) cc_final: 0.6785 (p0) REVERT: E 54 PHE cc_start: 0.8457 (m-80) cc_final: 0.8212 (m-80) REVERT: F 20 ASP cc_start: 0.8161 (m-30) cc_final: 0.7947 (m-30) REVERT: F 60 TYR cc_start: 0.6260 (m-80) cc_final: 0.6009 (m-10) REVERT: K 26 GLN cc_start: 0.6269 (pt0) cc_final: 0.6015 (pt0) REVERT: O 60 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8379 (tp-100) REVERT: P 28 LYS cc_start: 0.8939 (ptpt) cc_final: 0.8727 (ptpp) REVERT: I 75 VAL cc_start: 0.5152 (m) cc_final: 0.4948 (m) REVERT: J 143 LYS cc_start: 0.8186 (tttt) cc_final: 0.7881 (pptt) REVERT: N 58 ASP cc_start: 0.8345 (m-30) cc_final: 0.8088 (m-30) REVERT: S 9 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7326 (mptt) REVERT: B 89 MET cc_start: 0.4309 (tpp) cc_final: 0.3969 (tpp) REVERT: B 120 MET cc_start: 0.2972 (ppp) cc_final: 0.2212 (ppp) REVERT: B 143 ASP cc_start: 0.6679 (m-30) cc_final: 0.5824 (t0) REVERT: B 147 LYS cc_start: 0.5204 (tmtt) cc_final: 0.4707 (tttt) REVERT: c 146 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7933 (mt-10) REVERT: f 47 MET cc_start: 0.8393 (ptp) cc_final: 0.8154 (ptp) REVERT: f 87 LYS cc_start: 0.9203 (mtpp) cc_final: 0.8394 (tmmt) REVERT: f 171 THR cc_start: 0.8121 (p) cc_final: 0.7332 (p) REVERT: j 17 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8892 (mtpp) REVERT: j 45 ASP cc_start: 0.8268 (t0) cc_final: 0.8051 (t0) REVERT: j 120 GLU cc_start: 0.8063 (tt0) cc_final: 0.7827 (tt0) REVERT: l 116 GLU cc_start: 0.8718 (tp30) cc_final: 0.8503 (tp30) REVERT: o 38 THR cc_start: 0.8494 (t) cc_final: 0.8150 (m) REVERT: o 63 LYS cc_start: 0.8851 (tttt) cc_final: 0.8518 (ttpp) REVERT: o 82 ASP cc_start: 0.8905 (t0) cc_final: 0.8692 (t70) REVERT: o 83 LYS cc_start: 0.8908 (pttp) cc_final: 0.8570 (pttm) REVERT: q 33 ILE cc_start: 0.9259 (pt) cc_final: 0.9003 (pt) REVERT: t 43 ILE cc_start: 0.8870 (mm) cc_final: 0.8528 (mm) REVERT: t 82 ASP cc_start: 0.7733 (p0) cc_final: 0.7391 (p0) outliers start: 65 outliers final: 16 residues processed: 1598 average time/residue: 2.1563 time to fit residues: 4889.5418 Evaluate side-chains 1196 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1179 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain P residue 122 LYS Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain X residue 22 LYS Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain g residue 54 GLU Chi-restraints excluded: chain g residue 157 GLU Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain k residue 27 SER Chi-restraints excluded: chain r residue 3 LYS Chi-restraints excluded: chain u residue 95 VAL Chi-restraints excluded: chain u residue 180 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 854 optimal weight: 10.0000 chunk 767 optimal weight: 10.0000 chunk 425 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 517 optimal weight: 9.9990 chunk 409 optimal weight: 0.2980 chunk 793 optimal weight: 40.0000 chunk 306 optimal weight: 10.0000 chunk 482 optimal weight: 5.9990 chunk 590 optimal weight: 1.9990 chunk 919 optimal weight: 10.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 54 GLN D 191 ASN E 158 ASN E 168 GLN F 53 GLN H 16 ASN H 19 GLN H 24 GLN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN T 55 ASN T 74 ASN T 84 ASN G 27 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 GLN I 68 ASN I 122 ASN ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 GLN M 64 HIS N 52 GLN S 25 GLN ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 24 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN d 25 ASN d 55 GLN e 93 HIS g 74 ASN ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 HIS g 129 ASN g 141 GLN j 69 HIS ** k 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 133 GLN l 67 ASN m 31 HIS n 108 GLN o 56 GLN q 94 GLN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 ASN ** u 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 GLN w 17 ASN x 64 ASN y 19 ASN z 19 GLN ** 0 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 29 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.428 156591 Z= 0.331 Angle : 0.763 71.034 234458 Z= 0.378 Chirality : 0.040 1.452 29802 Planarity : 0.007 0.134 12568 Dihedral : 24.057 179.492 79512 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.47 % Favored : 94.05 % Rotamer: Outliers : 4.14 % Allowed : 16.82 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.00 (0.11), residues: 5646 helix: 1.26 (0.12), residues: 1863 sheet: -0.23 (0.15), residues: 1080 loop : -0.75 (0.12), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP c 214 HIS 0.015 0.001 HIS K 124 PHE 0.020 0.002 PHE K 67 TYR 0.019 0.002 TYR D 70 ARG 0.008 0.001 ARG s 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1197 time to evaluate : 6.254 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: D 126 ASN cc_start: 0.7772 (p0) cc_final: 0.7551 (p0) REVERT: E 54 PHE cc_start: 0.8548 (m-80) cc_final: 0.8328 (m-80) REVERT: E 83 ILE cc_start: 0.9094 (pp) cc_final: 0.8836 (pp) REVERT: F 2 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7537 (mpt-90) REVERT: F 20 ASP cc_start: 0.8182 (m-30) cc_final: 0.7128 (m-30) REVERT: F 27 LEU cc_start: 0.8541 (mt) cc_final: 0.8293 (mp) REVERT: H 5 ASP cc_start: 0.8105 (t0) cc_final: 0.7905 (t0) REVERT: H 73 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7575 (tpt170) REVERT: K 42 ASP cc_start: 0.8524 (t0) cc_final: 0.7671 (p0) REVERT: O 60 GLN cc_start: 0.8733 (tp-100) cc_final: 0.8429 (tp40) REVERT: P 12 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8466 (mtpm) REVERT: P 52 ASP cc_start: 0.8406 (t0) cc_final: 0.8158 (t70) REVERT: P 55 ARG cc_start: 0.8607 (mmm160) cc_final: 0.8277 (mmm-85) REVERT: J 143 LYS cc_start: 0.8203 (tttt) cc_final: 0.7754 (mttp) REVERT: M 15 HIS cc_start: 0.6563 (p-80) cc_final: 0.6302 (p-80) REVERT: N 45 VAL cc_start: 0.6784 (OUTLIER) cc_final: 0.6560 (p) REVERT: N 58 ASP cc_start: 0.8360 (m-30) cc_final: 0.8137 (m-30) REVERT: B 27 MET cc_start: 0.3393 (mmp) cc_final: 0.3165 (mmp) REVERT: B 143 ASP cc_start: 0.6738 (m-30) cc_final: 0.5964 (t0) REVERT: c 134 ARG cc_start: 0.8690 (ptm-80) cc_final: 0.8354 (ptm-80) REVERT: c 148 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7606 (mtt180) REVERT: d 23 GLU cc_start: 0.7823 (pp20) cc_final: 0.7609 (pp20) REVERT: f 73 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9084 (ttpp) REVERT: f 87 LYS cc_start: 0.9188 (mtpp) cc_final: 0.8383 (tmmt) REVERT: f 184 PHE cc_start: 0.8380 (m-80) cc_final: 0.8150 (m-80) REVERT: i 129 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: j 108 GLU cc_start: 0.6535 (mm-30) cc_final: 0.6330 (mp0) REVERT: n 28 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8829 (mtmt) REVERT: o 38 THR cc_start: 0.8903 (t) cc_final: 0.8668 (m) REVERT: o 82 ASP cc_start: 0.8938 (t0) cc_final: 0.8703 (t70) REVERT: o 112 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7793 (tp30) REVERT: q 24 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8427 (tttp) REVERT: r 3 LYS cc_start: 0.5810 (OUTLIER) cc_final: 0.5186 (ptmm) REVERT: t 82 ASP cc_start: 0.7821 (p0) cc_final: 0.7440 (p0) REVERT: 3 13 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8183 (mmmt) outliers start: 195 outliers final: 82 residues processed: 1274 average time/residue: 2.0862 time to fit residues: 3844.8802 Evaluate side-chains 1205 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1111 time to evaluate : 6.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 105 SER Chi-restraints excluded: chain O residue 70 LYS Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain G residue 189 ARG Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 71 LYS Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 171 MET Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain f residue 73 LYS Chi-restraints excluded: chain f residue 138 THR Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain g residue 113 HIS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 157 GLU Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain j residue 9 LYS Chi-restraints excluded: chain j residue 81 GLU Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ASP Chi-restraints excluded: chain k residue 131 SER Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 28 LYS Chi-restraints excluded: chain n residue 44 SER Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 112 GLU Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 24 LYS Chi-restraints excluded: chain r residue 3 LYS Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain s residue 81 THR Chi-restraints excluded: chain t residue 33 ARG Chi-restraints excluded: chain u residue 36 HIS Chi-restraints excluded: chain u residue 103 VAL Chi-restraints excluded: chain u residue 117 THR Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain x residue 62 GLU Chi-restraints excluded: chain 0 residue 16 CYS Chi-restraints excluded: chain 1 residue 20 SER Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 38 SER Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 3 residue 13 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 510 optimal weight: 9.9990 chunk 285 optimal weight: 30.0000 chunk 764 optimal weight: 10.0000 chunk 625 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 920 optimal weight: 10.0000 chunk 994 optimal weight: 10.0000 chunk 819 optimal weight: 10.0000 chunk 912 optimal weight: 8.9990 chunk 313 optimal weight: 0.0570 chunk 738 optimal weight: 10.0000 overall best weight: 7.0108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 66 GLN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN E 144 HIS E 168 GLN F 53 GLN H 16 ASN H 19 GLN K 34 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN T 55 ASN T 84 ASN ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 HIS ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN d 55 GLN e 93 HIS f 127 ASN ** g 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 74 ASN g 113 HIS g 129 ASN g 141 GLN ** k 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 67 ASN n 108 GLN p 20 GLN p 120 ASN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 ASN u 68 GLN x 64 ASN y 19 ASN 0 29 ASN ** 3 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.433 156591 Z= 0.419 Angle : 0.777 69.238 234458 Z= 0.388 Chirality : 0.043 1.458 29802 Planarity : 0.007 0.139 12568 Dihedral : 23.971 179.759 79484 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.60 % Favored : 93.92 % Rotamer: Outliers : 5.35 % Allowed : 19.07 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 5646 helix: 1.23 (0.12), residues: 1856 sheet: -0.33 (0.15), residues: 1095 loop : -0.83 (0.12), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP c 214 HIS 0.037 0.001 HIS g 113 PHE 0.016 0.002 PHE S 37 TYR 0.023 0.002 TYR D 70 ARG 0.013 0.001 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1167 time to evaluate : 6.123 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: E 46 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6588 (tttp) REVERT: E 53 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6831 (ptt90) REVERT: E 54 PHE cc_start: 0.8704 (m-80) cc_final: 0.8378 (m-80) REVERT: E 83 ILE cc_start: 0.9240 (pp) cc_final: 0.8973 (pp) REVERT: E 155 ASN cc_start: 0.8715 (t0) cc_final: 0.8473 (t0) REVERT: F 16 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8110 (tp30) REVERT: F 20 ASP cc_start: 0.8456 (m-30) cc_final: 0.7787 (m-30) REVERT: F 27 LEU cc_start: 0.8524 (mt) cc_final: 0.8260 (mp) REVERT: H 73 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7541 (tpt170) REVERT: K 42 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.7704 (p0) REVERT: O 6 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8782 (tttt) REVERT: O 60 GLN cc_start: 0.8778 (tp-100) cc_final: 0.7554 (tp-100) REVERT: O 63 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7720 (mtm180) REVERT: O 80 ILE cc_start: 0.9027 (pp) cc_final: 0.8751 (pt) REVERT: Q 1 MET cc_start: 0.1944 (OUTLIER) cc_final: 0.1616 (ptp) REVERT: T 7 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7779 (mm-40) REVERT: P 12 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8604 (mtpm) REVERT: P 52 ASP cc_start: 0.8410 (t0) cc_final: 0.8171 (t70) REVERT: P 55 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8360 (mmm-85) REVERT: G 4 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6912 (mptp) REVERT: G 161 MET cc_start: 0.6992 (mmt) cc_final: 0.6768 (tpp) REVERT: I 121 MET cc_start: 0.5212 (OUTLIER) cc_final: 0.4659 (tmm) REVERT: I 137 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7947 (ttp80) REVERT: J 143 LYS cc_start: 0.8243 (tttt) cc_final: 0.7797 (mttp) REVERT: J 147 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5692 (tt) REVERT: N 58 ASP cc_start: 0.8423 (m-30) cc_final: 0.8198 (m-30) REVERT: B 95 ARG cc_start: 0.3563 (ttt-90) cc_final: 0.1473 (ttt-90) REVERT: B 107 ILE cc_start: 0.5607 (OUTLIER) cc_final: 0.4816 (pp) REVERT: B 110 ARG cc_start: 0.4671 (OUTLIER) cc_final: 0.3871 (mmm160) REVERT: B 143 ASP cc_start: 0.6644 (m-30) cc_final: 0.5913 (t0) REVERT: B 153 ARG cc_start: 0.6797 (mtp-110) cc_final: 0.6533 (tpt170) REVERT: B 154 ASP cc_start: 0.7415 (m-30) cc_final: 0.6932 (p0) REVERT: B 157 LYS cc_start: 0.4981 (OUTLIER) cc_final: 0.3842 (mmmt) REVERT: c 134 ARG cc_start: 0.8736 (ptm-80) cc_final: 0.8402 (ptm160) REVERT: c 148 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7588 (mtt180) REVERT: d 109 GLU cc_start: 0.7677 (tp30) cc_final: 0.7374 (tp30) REVERT: f 47 MET cc_start: 0.8272 (ptp) cc_final: 0.7959 (ptp) REVERT: f 73 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9175 (ttpp) REVERT: f 87 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8496 (tmmt) REVERT: f 171 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.7783 (p) REVERT: f 184 PHE cc_start: 0.8398 (m-80) cc_final: 0.8125 (m-80) REVERT: g 113 HIS cc_start: 0.8373 (p-80) cc_final: 0.8112 (p90) REVERT: g 157 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7566 (pp20) REVERT: i 21 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: i 129 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: j 45 ASP cc_start: 0.8588 (t0) cc_final: 0.8177 (t0) REVERT: l 116 GLU cc_start: 0.8794 (tp30) cc_final: 0.8455 (tp30) REVERT: m 43 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8592 (mtt-85) REVERT: n 38 MET cc_start: 0.8738 (ttm) cc_final: 0.8516 (ttp) REVERT: n 66 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8439 (mtm) REVERT: o 82 ASP cc_start: 0.8961 (t0) cc_final: 0.8743 (t70) REVERT: o 109 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8293 (ptpp) REVERT: o 113 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7651 (ttp-170) REVERT: r 3 LYS cc_start: 0.5518 (OUTLIER) cc_final: 0.5177 (ptmm) REVERT: r 95 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: t 82 ASP cc_start: 0.7807 (p0) cc_final: 0.7216 (p0) REVERT: y 30 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8671 (mttm) outliers start: 252 outliers final: 119 residues processed: 1275 average time/residue: 2.0684 time to fit residues: 3824.3735 Evaluate side-chains 1244 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1097 time to evaluate : 6.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 25 VAL Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 189 ARG Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain I residue 137 ARG Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 88 MET Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 39 MET Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain c residue 32 SER Chi-restraints excluded: chain c residue 111 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 171 MET Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 73 LYS Chi-restraints excluded: chain f residue 138 THR Chi-restraints excluded: chain f residue 171 THR Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 157 GLU Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain i residue 21 GLU Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain j residue 9 LYS Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 THR Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 81 GLU Chi-restraints excluded: chain j residue 116 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ASP Chi-restraints excluded: chain k residue 131 SER Chi-restraints excluded: chain l residue 109 VAL Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 44 SER Chi-restraints excluded: chain n residue 66 MET Chi-restraints excluded: chain n residue 78 THR Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 109 LYS Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 3 LYS Chi-restraints excluded: chain r residue 4 THR Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain t residue 33 ARG Chi-restraints excluded: chain u residue 36 HIS Chi-restraints excluded: chain u residue 95 VAL Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain u residue 138 VAL Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 60 SER Chi-restraints excluded: chain y residue 30 LYS Chi-restraints excluded: chain 0 residue 16 CYS Chi-restraints excluded: chain 1 residue 20 SER Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 38 SER Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 62 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 909 optimal weight: 6.9990 chunk 692 optimal weight: 5.9990 chunk 477 optimal weight: 40.0000 chunk 101 optimal weight: 50.0000 chunk 439 optimal weight: 3.9990 chunk 618 optimal weight: 3.9990 chunk 923 optimal weight: 8.9990 chunk 978 optimal weight: 10.0000 chunk 482 optimal weight: 9.9990 chunk 875 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 66 GLN ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN E 168 GLN F 53 GLN H 16 ASN H 18 ASN H 24 GLN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN T 55 ASN T 74 ASN ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 86 GLN I 129 ASN I 148 ASN ** J 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN d 55 GLN ** g 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 74 ASN g 75 ASN ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 129 ASN g 141 GLN ** k 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 67 ASN ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 GLN p 20 GLN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 GLN x 64 ASN y 19 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.433 156591 Z= 0.366 Angle : 0.750 69.653 234458 Z= 0.374 Chirality : 0.041 1.487 29802 Planarity : 0.006 0.136 12568 Dihedral : 23.936 179.996 79484 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.60 % Favored : 93.91 % Rotamer: Outliers : 5.08 % Allowed : 21.30 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.10 (0.11), residues: 5646 helix: 1.17 (0.12), residues: 1878 sheet: -0.22 (0.15), residues: 1070 loop : -0.86 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP c 214 HIS 0.015 0.001 HIS K 124 PHE 0.024 0.002 PHE T 35 TYR 0.024 0.002 TYR D 70 ARG 0.010 0.001 ARG s 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1175 time to evaluate : 6.263 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: D 152 ILE cc_start: 0.8465 (mm) cc_final: 0.8174 (tp) REVERT: E 38 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.9025 (t) REVERT: E 83 ILE cc_start: 0.9256 (pp) cc_final: 0.8971 (pp) REVERT: E 88 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8462 (mm-30) REVERT: F 16 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8120 (tp30) REVERT: F 20 ASP cc_start: 0.8435 (m-30) cc_final: 0.8024 (m-30) REVERT: H 73 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7501 (tpt170) REVERT: K 42 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7664 (p0) REVERT: K 62 ARG cc_start: 0.8726 (ptp-110) cc_final: 0.8284 (ttm-80) REVERT: K 99 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8015 (ttp-170) REVERT: O 36 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7840 (mt-10) REVERT: O 60 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8424 (tp40) REVERT: O 80 ILE cc_start: 0.8977 (pp) cc_final: 0.8727 (pt) REVERT: Q 1 MET cc_start: 0.2373 (OUTLIER) cc_final: 0.1431 (ptp) REVERT: R 64 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: P 52 ASP cc_start: 0.8336 (t0) cc_final: 0.8134 (t70) REVERT: P 55 ARG cc_start: 0.8745 (mmm160) cc_final: 0.8339 (mmm-85) REVERT: G 4 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6934 (mptp) REVERT: G 161 MET cc_start: 0.7020 (mmt) cc_final: 0.6796 (tpp) REVERT: I 121 MET cc_start: 0.5382 (OUTLIER) cc_final: 0.4772 (tmm) REVERT: J 143 LYS cc_start: 0.8171 (tttt) cc_final: 0.7788 (mttp) REVERT: J 147 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5601 (tt) REVERT: N 59 HIS cc_start: 0.7444 (t70) cc_final: 0.7096 (t70) REVERT: U 12 ASP cc_start: 0.6612 (OUTLIER) cc_final: 0.6387 (t70) REVERT: B 27 MET cc_start: 0.3959 (mmp) cc_final: 0.3699 (mmp) REVERT: B 95 ARG cc_start: 0.3273 (ttt-90) cc_final: 0.2195 (ttp-170) REVERT: B 110 ARG cc_start: 0.4654 (OUTLIER) cc_final: 0.4343 (mmm160) REVERT: B 140 ARG cc_start: 0.4794 (ttt-90) cc_final: 0.4155 (ptm160) REVERT: B 153 ARG cc_start: 0.6890 (mtp-110) cc_final: 0.6493 (tpt170) REVERT: c 134 ARG cc_start: 0.8711 (ptm-80) cc_final: 0.8361 (ptm160) REVERT: c 148 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7598 (mtt180) REVERT: d 109 GLU cc_start: 0.7642 (tp30) cc_final: 0.7411 (tp30) REVERT: f 67 THR cc_start: 0.9249 (p) cc_final: 0.9008 (t) REVERT: f 73 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9167 (ttpp) REVERT: f 87 LYS cc_start: 0.9263 (mtpp) cc_final: 0.8434 (tmmt) REVERT: f 114 THR cc_start: 0.8956 (m) cc_final: 0.8676 (p) REVERT: f 184 PHE cc_start: 0.8385 (m-80) cc_final: 0.7952 (m-80) REVERT: g 95 TYR cc_start: 0.8491 (m-10) cc_final: 0.8284 (m-10) REVERT: i 21 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: i 22 ASP cc_start: 0.8251 (m-30) cc_final: 0.7994 (m-30) REVERT: i 129 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: j 45 ASP cc_start: 0.8563 (t0) cc_final: 0.8186 (t0) REVERT: k 133 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: m 43 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8578 (mtt-85) REVERT: n 66 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8045 (mtm) REVERT: n 87 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9064 (mp) REVERT: r 95 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: s 27 ASP cc_start: 0.8058 (m-30) cc_final: 0.7730 (m-30) REVERT: t 82 ASP cc_start: 0.7788 (p0) cc_final: 0.7145 (p0) REVERT: y 30 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8683 (mttm) REVERT: 0 45 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8675 (ttp80) outliers start: 239 outliers final: 126 residues processed: 1283 average time/residue: 2.0542 time to fit residues: 3838.4350 Evaluate side-chains 1258 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1108 time to evaluate : 6.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 99 ARG Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain O residue 25 VAL Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain J residue 71 LYS Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 39 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain d residue 171 MET Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 73 LYS Chi-restraints excluded: chain f residue 138 THR Chi-restraints excluded: chain f residue 173 GLU Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 21 GLU Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain j residue 9 LYS Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 81 GLU Chi-restraints excluded: chain j residue 112 MET Chi-restraints excluded: chain j residue 116 SER Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ASP Chi-restraints excluded: chain k residue 131 SER Chi-restraints excluded: chain k residue 133 GLN Chi-restraints excluded: chain l residue 113 VAL Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 44 SER Chi-restraints excluded: chain n residue 66 MET Chi-restraints excluded: chain n residue 78 THR Chi-restraints excluded: chain n residue 87 ILE Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 36 THR Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain r residue 98 THR Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain t residue 33 ARG Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain u residue 138 VAL Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 60 SER Chi-restraints excluded: chain y residue 30 LYS Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain 0 residue 16 CYS Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 45 ARG Chi-restraints excluded: chain 1 residue 20 SER Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 38 SER Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 THR Chi-restraints excluded: chain 4 residue 41 CYS Chi-restraints excluded: chain 4 residue 62 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 814 optimal weight: 50.0000 chunk 555 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 728 optimal weight: 10.0000 chunk 403 optimal weight: 0.9990 chunk 834 optimal weight: 10.0000 chunk 676 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 499 optimal weight: 4.9990 chunk 878 optimal weight: 20.0000 chunk 246 optimal weight: 20.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 66 GLN D 191 ASN E 158 ASN E 168 GLN F 53 GLN F 73 GLN H 16 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN T 55 ASN G 8 HIS I 106 ASN J 169 GLN ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN g 34 ASN ** g 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 74 ASN g 75 ASN g 113 HIS g 129 ASN g 141 GLN k 75 GLN ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 GLN p 20 GLN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 GLN y 19 ASN ** 0 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.433 156591 Z= 0.358 Angle : 0.751 69.385 234458 Z= 0.374 Chirality : 0.041 1.488 29802 Planarity : 0.006 0.135 12568 Dihedral : 23.910 179.946 79472 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.60 % Favored : 93.96 % Rotamer: Outliers : 5.69 % Allowed : 22.43 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.15 (0.11), residues: 5646 helix: 1.09 (0.12), residues: 1872 sheet: -0.24 (0.15), residues: 1077 loop : -0.86 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 214 HIS 0.011 0.001 HIS K 124 PHE 0.026 0.002 PHE U 10 TYR 0.024 0.002 TYR D 70 ARG 0.015 0.001 ARG K 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1152 time to evaluate : 6.114 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: D 171 ASN cc_start: 0.7801 (p0) cc_final: 0.7125 (p0) REVERT: D 191 ASN cc_start: 0.8122 (t0) cc_final: 0.7886 (t0) REVERT: E 38 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9073 (t) REVERT: E 83 ILE cc_start: 0.9275 (pp) cc_final: 0.9003 (pp) REVERT: E 88 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8458 (mm-30) REVERT: F 16 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: F 20 ASP cc_start: 0.8211 (m-30) cc_final: 0.7835 (m-30) REVERT: H 73 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7484 (tpt170) REVERT: K 62 ARG cc_start: 0.8791 (ptp-110) cc_final: 0.8343 (ttm-80) REVERT: O 60 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8422 (tp40) REVERT: O 80 ILE cc_start: 0.9005 (pp) cc_final: 0.8769 (pt) REVERT: Q 1 MET cc_start: 0.2504 (OUTLIER) cc_final: 0.1651 (ptp) REVERT: R 64 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6657 (tt0) REVERT: T 36 ARG cc_start: 0.8852 (mpt-90) cc_final: 0.8586 (mpt-90) REVERT: P 55 ARG cc_start: 0.8730 (mmm160) cc_final: 0.8318 (mmm-85) REVERT: G 4 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7040 (mptp) REVERT: G 113 GLN cc_start: 0.7989 (tp40) cc_final: 0.7590 (tp40) REVERT: G 162 SER cc_start: 0.8445 (t) cc_final: 0.8238 (m) REVERT: I 121 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.5214 (tmm) REVERT: I 122 ASN cc_start: 0.6496 (m-40) cc_final: 0.6146 (m-40) REVERT: J 143 LYS cc_start: 0.8134 (tttt) cc_final: 0.7759 (mptp) REVERT: J 147 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.5667 (tt) REVERT: N 59 HIS cc_start: 0.7380 (t70) cc_final: 0.7057 (t70) REVERT: U 12 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6738 (t70) REVERT: B 106 THR cc_start: 0.6513 (p) cc_final: 0.6084 (t) REVERT: B 140 ARG cc_start: 0.4786 (ttt-90) cc_final: 0.4350 (ptm160) REVERT: B 153 ARG cc_start: 0.6735 (mtp-110) cc_final: 0.6338 (tpt170) REVERT: B 154 ASP cc_start: 0.7636 (m-30) cc_final: 0.7120 (p0) REVERT: c 134 ARG cc_start: 0.8691 (ptm-80) cc_final: 0.8306 (ptm160) REVERT: c 148 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7601 (mtt180) REVERT: d 87 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8371 (mt-10) REVERT: d 109 GLU cc_start: 0.7656 (tp30) cc_final: 0.7455 (tp30) REVERT: f 73 LYS cc_start: 0.9512 (OUTLIER) cc_final: 0.9196 (ttpp) REVERT: f 87 LYS cc_start: 0.9250 (mtpp) cc_final: 0.8448 (tmmt) REVERT: f 143 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: i 21 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: i 22 ASP cc_start: 0.8248 (m-30) cc_final: 0.7971 (m-30) REVERT: i 129 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: i 141 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: j 45 ASP cc_start: 0.8587 (t0) cc_final: 0.8190 (t0) REVERT: l 67 ASN cc_start: 0.9257 (m110) cc_final: 0.9025 (m110) REVERT: m 43 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8593 (mtt-85) REVERT: n 24 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.7336 (ptp90) REVERT: n 66 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8124 (mtm) REVERT: o 19 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7645 (tm-30) REVERT: o 94 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.7826 (mtp85) REVERT: o 109 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8394 (ptpp) REVERT: q 24 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8043 (tttp) REVERT: r 95 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: t 82 ASP cc_start: 0.7834 (p0) cc_final: 0.7200 (p0) REVERT: u 69 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8646 (ptpt) REVERT: x 70 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6552 (t0) REVERT: y 30 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8653 (mttm) REVERT: 0 33 ASN cc_start: 0.9041 (m-40) cc_final: 0.8815 (m-40) REVERT: 0 39 MET cc_start: 0.8720 (mtp) cc_final: 0.8520 (mtp) REVERT: 0 45 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8708 (ttp80) REVERT: 4 1 MET cc_start: 0.7449 (mmt) cc_final: 0.7214 (tpp) outliers start: 268 outliers final: 147 residues processed: 1275 average time/residue: 2.0450 time to fit residues: 3791.6532 Evaluate side-chains 1292 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1118 time to evaluate : 6.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain O residue 25 VAL Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 64 GLU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 GLU Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 56 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 39 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain c residue 71 ASP Chi-restraints excluded: chain c residue 111 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain d residue 171 MET Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 73 LYS Chi-restraints excluded: chain f residue 138 THR Chi-restraints excluded: chain f residue 143 GLU Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain g residue 113 HIS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 21 GLU Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 86 VAL Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 9 LYS Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 THR Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 81 GLU Chi-restraints excluded: chain j residue 112 MET Chi-restraints excluded: chain j residue 116 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ASP Chi-restraints excluded: chain k residue 131 SER Chi-restraints excluded: chain l residue 54 MET Chi-restraints excluded: chain l residue 113 VAL Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 24 ARG Chi-restraints excluded: chain n residue 44 SER Chi-restraints excluded: chain n residue 66 MET Chi-restraints excluded: chain n residue 73 MET Chi-restraints excluded: chain n residue 78 THR Chi-restraints excluded: chain o residue 7 GLU Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain o residue 109 LYS Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 24 LYS Chi-restraints excluded: chain q residue 36 THR Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain r residue 98 THR Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain t residue 33 ARG Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 69 LYS Chi-restraints excluded: chain u residue 95 VAL Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain u residue 157 LEU Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 60 SER Chi-restraints excluded: chain x residue 70 ASP Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 30 LYS Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain 0 residue 16 CYS Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 45 ARG Chi-restraints excluded: chain 1 residue 20 SER Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 38 SER Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 THR Chi-restraints excluded: chain 4 residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 329 optimal weight: 20.0000 chunk 880 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 574 optimal weight: 0.7980 chunk 241 optimal weight: 20.0000 chunk 979 optimal weight: 8.9990 chunk 812 optimal weight: 50.0000 chunk 453 optimal weight: 20.0000 chunk 81 optimal weight: 40.0000 chunk 323 optimal weight: 30.0000 chunk 514 optimal weight: 8.9990 overall best weight: 9.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 66 GLN D 108 GLN E 158 ASN E 168 GLN F 53 GLN F 73 GLN H 16 ASN H 120 GLN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN T 74 ASN T 84 ASN ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 HIS G 137 GLN I 41 ASN I 106 ASN ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 GLN ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN d 55 GLN ** f 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 ASN ** g 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 74 ASN g 75 ASN g 113 HIS g 129 ASN ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 GLN l 67 ASN l 123 HIS ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 GLN p 20 GLN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 GLN x 64 ASN y 19 ASN ** 0 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.433 156591 Z= 0.553 Angle : 0.836 69.250 234458 Z= 0.415 Chirality : 0.047 1.477 29802 Planarity : 0.007 0.143 12568 Dihedral : 23.929 179.774 79472 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.20 % Favored : 93.36 % Rotamer: Outliers : 6.22 % Allowed : 23.17 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.11), residues: 5646 helix: 0.89 (0.12), residues: 1877 sheet: -0.29 (0.16), residues: 1040 loop : -0.99 (0.12), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 214 HIS 0.043 0.002 HIS g 113 PHE 0.020 0.002 PHE P 83 TYR 0.027 0.002 TYR o 98 ARG 0.013 0.001 ARG s 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1118 time to evaluate : 6.067 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: E 83 ILE cc_start: 0.9224 (pp) cc_final: 0.8955 (pp) REVERT: E 88 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8484 (mm-30) REVERT: F 16 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8186 (tp30) REVERT: F 20 ASP cc_start: 0.8246 (m-30) cc_final: 0.7856 (m-30) REVERT: F 73 GLN cc_start: 0.8388 (mt0) cc_final: 0.8121 (mt0) REVERT: F 86 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7860 (mpp) REVERT: H 73 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7467 (tpt170) REVERT: H 75 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8432 (mpt180) REVERT: K 42 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7547 (p0) REVERT: K 62 ARG cc_start: 0.8849 (ptp-110) cc_final: 0.8302 (ttm-80) REVERT: L 95 TYR cc_start: 0.8969 (m-80) cc_final: 0.8709 (m-80) REVERT: O 60 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8492 (tp-100) REVERT: O 68 ILE cc_start: 0.9196 (mt) cc_final: 0.8925 (mp) REVERT: O 80 ILE cc_start: 0.8996 (pp) cc_final: 0.8786 (pt) REVERT: Q 1 MET cc_start: 0.2477 (OUTLIER) cc_final: 0.1763 (ptp) REVERT: R 52 GLN cc_start: 0.8814 (tp40) cc_final: 0.8519 (tt0) REVERT: P 52 ASP cc_start: 0.8431 (t70) cc_final: 0.8172 (t0) REVERT: G 4 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6720 (mtmm) REVERT: I 121 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5354 (tmm) REVERT: J 143 LYS cc_start: 0.8257 (tttt) cc_final: 0.7923 (mttp) REVERT: J 147 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6286 (tt) REVERT: N 59 HIS cc_start: 0.7593 (t70) cc_final: 0.7352 (t70) REVERT: B 27 MET cc_start: 0.3919 (mmp) cc_final: 0.3651 (mmp) REVERT: B 110 ARG cc_start: 0.4859 (mmm160) cc_final: 0.4314 (mmm160) REVERT: B 153 ARG cc_start: 0.6845 (mtp-110) cc_final: 0.6455 (tpt170) REVERT: B 154 ASP cc_start: 0.7709 (m-30) cc_final: 0.7179 (p0) REVERT: B 216 ARG cc_start: 0.5046 (mmm160) cc_final: 0.4788 (mmt-90) REVERT: B 227 MET cc_start: 0.4033 (ptm) cc_final: 0.3825 (ptm) REVERT: c 101 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: c 134 ARG cc_start: 0.8734 (ptm-80) cc_final: 0.8523 (ptm-80) REVERT: c 148 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7626 (mtt180) REVERT: d 130 ARG cc_start: 0.9441 (OUTLIER) cc_final: 0.8959 (ptm160) REVERT: e 174 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8649 (mm) REVERT: f 73 LYS cc_start: 0.9532 (OUTLIER) cc_final: 0.9219 (ttpp) REVERT: f 87 LYS cc_start: 0.9275 (mtpp) cc_final: 0.8503 (tmmt) REVERT: f 114 THR cc_start: 0.9019 (m) cc_final: 0.8774 (p) REVERT: g 72 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8899 (tt) REVERT: i 21 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: i 22 ASP cc_start: 0.8310 (m-30) cc_final: 0.8031 (m-30) REVERT: i 129 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: m 43 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8642 (mtt-85) REVERT: n 24 ARG cc_start: 0.9453 (OUTLIER) cc_final: 0.6841 (ttp80) REVERT: n 66 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8117 (mtm) REVERT: o 19 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7645 (tm-30) REVERT: o 94 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.7816 (mtp85) REVERT: o 109 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8532 (ptpp) REVERT: r 95 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: t 82 ASP cc_start: 0.7913 (p0) cc_final: 0.7282 (p0) REVERT: u 45 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8720 (mt) REVERT: u 69 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8662 (ptpt) REVERT: u 152 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6178 (pp) REVERT: x 70 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6725 (t0) REVERT: y 30 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8639 (mttm) REVERT: 0 11 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8900 (mtpt) REVERT: 0 45 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8761 (ttp80) outliers start: 293 outliers final: 165 residues processed: 1256 average time/residue: 2.0941 time to fit residues: 3832.5988 Evaluate side-chains 1294 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1098 time to evaluate : 6.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain O residue 25 VAL Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain U residue 39 MET Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain c residue 32 SER Chi-restraints excluded: chain c residue 71 ASP Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain c residue 111 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain d residue 130 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 174 LEU Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 73 LYS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 138 THR Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 113 HIS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 21 GLU Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 86 VAL Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain j residue 9 LYS Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 THR Chi-restraints excluded: chain j residue 63 VAL Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 81 GLU Chi-restraints excluded: chain j residue 116 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ASP Chi-restraints excluded: chain k residue 131 SER Chi-restraints excluded: chain l residue 89 THR Chi-restraints excluded: chain l residue 113 VAL Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 24 ARG Chi-restraints excluded: chain n residue 44 SER Chi-restraints excluded: chain n residue 53 ASP Chi-restraints excluded: chain n residue 66 MET Chi-restraints excluded: chain n residue 73 MET Chi-restraints excluded: chain n residue 78 THR Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain o residue 109 LYS Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 36 THR Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain r residue 98 THR Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain t residue 33 ARG Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 69 LYS Chi-restraints excluded: chain u residue 95 VAL Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain u residue 152 ILE Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 60 SER Chi-restraints excluded: chain x residue 70 ASP Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 30 LYS Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain 0 residue 11 LYS Chi-restraints excluded: chain 0 residue 16 CYS Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 45 ARG Chi-restraints excluded: chain 1 residue 20 SER Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 38 SER Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 THR Chi-restraints excluded: chain 4 residue 13 THR Chi-restraints excluded: chain 4 residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 944 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 557 optimal weight: 6.9990 chunk 715 optimal weight: 7.9990 chunk 554 optimal weight: 5.9990 chunk 824 optimal weight: 6.9990 chunk 546 optimal weight: 6.9990 chunk 975 optimal weight: 5.9990 chunk 610 optimal weight: 4.9990 chunk 594 optimal weight: 1.9990 chunk 450 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 66 GLN D 108 GLN D 178 HIS E 158 ASN E 168 GLN F 53 GLN H 16 ASN H 120 GLN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN G 137 GLN I 41 ASN I 106 ASN ** J 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 GLN ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 ASN ** g 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 ASN g 113 HIS g 129 ASN ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 GLN ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 GLN p 20 GLN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 ASN ** u 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 GLN y 19 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.433 156591 Z= 0.312 Angle : 0.742 69.485 234458 Z= 0.370 Chirality : 0.040 1.483 29802 Planarity : 0.006 0.133 12568 Dihedral : 23.931 179.517 79472 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.56 % Favored : 94.01 % Rotamer: Outliers : 5.05 % Allowed : 25.36 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.23 (0.11), residues: 5646 helix: 1.03 (0.12), residues: 1872 sheet: -0.26 (0.16), residues: 1075 loop : -0.91 (0.12), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 214 HIS 0.023 0.001 HIS g 113 PHE 0.019 0.002 PHE E 54 TYR 0.026 0.002 TYR D 70 ARG 0.014 0.000 ARG K 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1394 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1156 time to evaluate : 6.211 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: E 38 VAL cc_start: 0.9370 (OUTLIER) cc_final: 0.9111 (t) REVERT: E 83 ILE cc_start: 0.9240 (pp) cc_final: 0.8965 (pp) REVERT: E 88 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8459 (mm-30) REVERT: F 3 LYS cc_start: 0.7850 (pmtt) cc_final: 0.7634 (ptmt) REVERT: F 16 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: F 20 ASP cc_start: 0.8136 (m-30) cc_final: 0.7710 (m-30) REVERT: F 86 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7840 (mpp) REVERT: H 73 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7411 (tpt170) REVERT: K 62 ARG cc_start: 0.8783 (ptp-110) cc_final: 0.8278 (ttm-80) REVERT: L 95 TYR cc_start: 0.8959 (m-80) cc_final: 0.8677 (m-80) REVERT: O 60 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8470 (tp40) REVERT: O 80 ILE cc_start: 0.8972 (pp) cc_final: 0.8764 (pt) REVERT: Q 1 MET cc_start: 0.2403 (OUTLIER) cc_final: 0.1517 (ptp) REVERT: R 52 GLN cc_start: 0.8729 (tp40) cc_final: 0.8466 (tt0) REVERT: T 36 ARG cc_start: 0.8862 (mpt-90) cc_final: 0.8656 (mpt-90) REVERT: G 4 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.6715 (mtmm) REVERT: G 113 GLN cc_start: 0.8133 (tp40) cc_final: 0.7920 (tp40) REVERT: I 121 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5506 (tmm) REVERT: J 147 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6438 (tt) REVERT: N 59 HIS cc_start: 0.7604 (t70) cc_final: 0.7330 (t70) REVERT: B 27 MET cc_start: 0.3818 (mmp) cc_final: 0.3594 (mmp) REVERT: B 153 ARG cc_start: 0.6751 (mtp-110) cc_final: 0.6454 (tpt170) REVERT: B 154 ASP cc_start: 0.7679 (m-30) cc_final: 0.7172 (p0) REVERT: B 216 ARG cc_start: 0.4963 (mmm160) cc_final: 0.4644 (mmt-90) REVERT: B 227 MET cc_start: 0.3998 (ptm) cc_final: 0.3774 (ptm) REVERT: c 101 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: c 134 ARG cc_start: 0.8663 (ptm-80) cc_final: 0.8355 (ptm-80) REVERT: c 148 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7555 (mtt180) REVERT: d 87 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8355 (mt-10) REVERT: d 109 GLU cc_start: 0.7602 (tp30) cc_final: 0.7402 (tp30) REVERT: f 73 LYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9220 (ttpp) REVERT: f 87 LYS cc_start: 0.9252 (mtpp) cc_final: 0.8448 (tmmt) REVERT: f 114 THR cc_start: 0.9003 (m) cc_final: 0.8753 (p) REVERT: f 157 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7889 (ptm-80) REVERT: f 184 PHE cc_start: 0.8248 (m-80) cc_final: 0.7587 (m-80) REVERT: g 72 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8918 (tt) REVERT: g 75 ASN cc_start: 0.8519 (m-40) cc_final: 0.8149 (m110) REVERT: i 80 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6930 (ptp-170) REVERT: i 129 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: i 141 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: j 105 GLU cc_start: 0.8915 (mp0) cc_final: 0.8515 (mp0) REVERT: l 111 GLU cc_start: 0.8116 (tp30) cc_final: 0.7823 (tp30) REVERT: m 43 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8548 (mtt-85) REVERT: n 24 ARG cc_start: 0.9395 (OUTLIER) cc_final: 0.7357 (ptp90) REVERT: o 63 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8646 (ttmm) REVERT: q 24 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8035 (tttp) REVERT: r 95 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: t 82 ASP cc_start: 0.7823 (p0) cc_final: 0.7249 (p0) REVERT: u 45 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8668 (mt) REVERT: u 69 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8652 (ptpt) REVERT: y 30 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8604 (mttm) REVERT: 0 11 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8910 (mtpt) REVERT: 0 45 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8712 (ttp80) outliers start: 238 outliers final: 140 residues processed: 1267 average time/residue: 2.0435 time to fit residues: 3769.8271 Evaluate side-chains 1288 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1121 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain U residue 39 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain c residue 111 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain f residue 73 LYS Chi-restraints excluded: chain f residue 138 THR Chi-restraints excluded: chain f residue 157 ARG Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 86 VAL Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 9 LYS Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain j residue 116 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ASP Chi-restraints excluded: chain k residue 131 SER Chi-restraints excluded: chain l residue 89 THR Chi-restraints excluded: chain l residue 113 VAL Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 24 ARG Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 44 SER Chi-restraints excluded: chain n residue 73 MET Chi-restraints excluded: chain n residue 78 THR Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 24 LYS Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 36 THR Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain t residue 33 ARG Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 69 LYS Chi-restraints excluded: chain u residue 95 VAL Chi-restraints excluded: chain u residue 121 THR Chi-restraints excluded: chain u residue 157 LEU Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 60 SER Chi-restraints excluded: chain y residue 30 LYS Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain 0 residue 11 LYS Chi-restraints excluded: chain 0 residue 16 CYS Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 35 ASP Chi-restraints excluded: chain 0 residue 45 ARG Chi-restraints excluded: chain 1 residue 20 SER Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 38 SER Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 THR Chi-restraints excluded: chain 4 residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 603 optimal weight: 1.9990 chunk 389 optimal weight: 7.9990 chunk 582 optimal weight: 0.8980 chunk 293 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 620 optimal weight: 9.9990 chunk 664 optimal weight: 9.9990 chunk 482 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 766 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 66 GLN D 108 GLN D 193 GLN E 158 ASN E 168 GLN F 53 GLN F 73 GLN H 16 ASN H 18 ASN H 120 GLN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN Q 58 ASN T 74 ASN ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN I 41 ASN I 106 ASN J 83 ASN ** J 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN d 55 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 ASN ** g 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 129 ASN ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 GLN l 67 ASN ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 GLN p 20 GLN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 ASN u 36 HIS u 68 GLN y 19 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.433 156591 Z= 0.340 Angle : 0.753 69.408 234458 Z= 0.374 Chirality : 0.040 1.487 29802 Planarity : 0.006 0.135 12568 Dihedral : 23.899 179.988 79472 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.06 % Favored : 93.52 % Rotamer: Outliers : 5.08 % Allowed : 25.84 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.11), residues: 5646 helix: 0.97 (0.12), residues: 1872 sheet: -0.25 (0.16), residues: 1074 loop : -0.90 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 214 HIS 0.010 0.001 HIS L 72 PHE 0.019 0.002 PHE P 83 TYR 0.028 0.002 TYR D 70 ARG 0.015 0.001 ARG K 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1133 time to evaluate : 6.097 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: E 38 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9082 (t) REVERT: E 83 ILE cc_start: 0.9221 (pp) cc_final: 0.8943 (pp) REVERT: E 88 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8473 (mm-30) REVERT: F 86 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7795 (mpp) REVERT: H 73 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7436 (tpt170) REVERT: K 62 ARG cc_start: 0.8799 (ptp-110) cc_final: 0.8291 (ttm-80) REVERT: L 18 LYS cc_start: 0.8316 (tmtp) cc_final: 0.8078 (tmtm) REVERT: L 95 TYR cc_start: 0.8957 (m-80) cc_final: 0.8687 (m-80) REVERT: O 60 GLN cc_start: 0.8707 (tp-100) cc_final: 0.7455 (tp40) REVERT: O 63 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7553 (mtm180) REVERT: O 80 ILE cc_start: 0.8961 (pp) cc_final: 0.8724 (pt) REVERT: Q 1 MET cc_start: 0.2513 (OUTLIER) cc_final: 0.1831 (ptp) REVERT: R 52 GLN cc_start: 0.8736 (tp40) cc_final: 0.8465 (tt0) REVERT: T 77 SER cc_start: 0.8683 (t) cc_final: 0.8448 (t) REVERT: G 4 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6728 (mtmm) REVERT: G 113 GLN cc_start: 0.8123 (tp40) cc_final: 0.7917 (tp40) REVERT: I 121 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5813 (tmm) REVERT: J 147 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6449 (tt) REVERT: N 59 HIS cc_start: 0.7631 (t70) cc_final: 0.7382 (t70) REVERT: B 153 ARG cc_start: 0.6775 (mtp-110) cc_final: 0.6490 (tpt170) REVERT: B 154 ASP cc_start: 0.7704 (m-30) cc_final: 0.7177 (p0) REVERT: B 216 ARG cc_start: 0.4985 (mmm160) cc_final: 0.4731 (mmt-90) REVERT: c 101 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: c 134 ARG cc_start: 0.8675 (ptm-80) cc_final: 0.8373 (ptm-80) REVERT: c 148 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7582 (mtt180) REVERT: d 87 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8358 (mt-10) REVERT: d 109 GLU cc_start: 0.7616 (tp30) cc_final: 0.7342 (tp30) REVERT: d 130 ARG cc_start: 0.9395 (OUTLIER) cc_final: 0.8929 (ptm160) REVERT: f 73 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9230 (ttpp) REVERT: f 87 LYS cc_start: 0.9301 (mtpp) cc_final: 0.8503 (tmmt) REVERT: f 114 THR cc_start: 0.8997 (m) cc_final: 0.8749 (p) REVERT: f 184 PHE cc_start: 0.8383 (m-80) cc_final: 0.7620 (m-80) REVERT: i 80 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7175 (ptp-170) REVERT: i 129 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: i 141 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: l 32 TYR cc_start: 0.9111 (m-80) cc_final: 0.8775 (m-80) REVERT: l 111 GLU cc_start: 0.8129 (tp30) cc_final: 0.7888 (tp30) REVERT: m 43 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8591 (mtt-85) REVERT: n 24 ARG cc_start: 0.9407 (OUTLIER) cc_final: 0.7344 (ptp90) REVERT: n 28 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8580 (mtmt) REVERT: n 118 ASP cc_start: 0.8343 (m-30) cc_final: 0.8119 (m-30) REVERT: o 19 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7623 (tm-30) REVERT: o 63 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8577 (ttmm) REVERT: o 94 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.7807 (mtp85) REVERT: q 24 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8054 (tttp) REVERT: r 95 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: t 82 ASP cc_start: 0.7848 (p0) cc_final: 0.7246 (p0) REVERT: u 45 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8673 (mt) REVERT: x 70 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6671 (t0) REVERT: y 30 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8643 (mttm) REVERT: 0 11 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8892 (mtpt) REVERT: 0 45 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.8716 (ttp80) outliers start: 239 outliers final: 147 residues processed: 1251 average time/residue: 2.0714 time to fit residues: 3774.2237 Evaluate side-chains 1284 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1109 time to evaluate : 6.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 86 MET Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 23 LYS Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain c residue 95 LEU Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain c residue 111 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain d residue 130 ARG Chi-restraints excluded: chain d residue 167 MET Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain f residue 73 LYS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 138 THR Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 86 VAL Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 THR Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain j residue 116 SER Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ASP Chi-restraints excluded: chain k residue 131 SER Chi-restraints excluded: chain l residue 54 MET Chi-restraints excluded: chain l residue 89 THR Chi-restraints excluded: chain l residue 113 VAL Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 24 ARG Chi-restraints excluded: chain n residue 28 LYS Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 44 SER Chi-restraints excluded: chain n residue 73 MET Chi-restraints excluded: chain n residue 78 THR Chi-restraints excluded: chain o residue 7 GLU Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 5 VAL Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 24 LYS Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 36 THR Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain r residue 98 THR Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain t residue 33 ARG Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 95 VAL Chi-restraints excluded: chain u residue 96 ARG Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 60 SER Chi-restraints excluded: chain x residue 70 ASP Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 30 LYS Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain 0 residue 11 LYS Chi-restraints excluded: chain 0 residue 16 CYS Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 45 ARG Chi-restraints excluded: chain 1 residue 20 SER Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 38 SER Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 THR Chi-restraints excluded: chain 4 residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 887 optimal weight: 10.0000 chunk 934 optimal weight: 10.0000 chunk 852 optimal weight: 10.0000 chunk 908 optimal weight: 8.9990 chunk 547 optimal weight: 0.9990 chunk 395 optimal weight: 0.6980 chunk 713 optimal weight: 10.0000 chunk 278 optimal weight: 0.8980 chunk 821 optimal weight: 10.0000 chunk 859 optimal weight: 10.0000 chunk 905 optimal weight: 8.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 66 GLN ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN E 158 ASN E 168 GLN F 53 GLN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN T 74 ASN G 137 GLN I 41 ASN I 106 ASN ** J 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN d 55 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 ASN ** g 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 129 ASN ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 GLN l 67 ASN ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 GLN p 20 GLN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 ASN u 68 GLN y 19 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.433 156591 Z= 0.286 Angle : 0.742 69.567 234458 Z= 0.369 Chirality : 0.039 1.484 29802 Planarity : 0.006 0.132 12568 Dihedral : 23.921 179.850 79472 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.83 % Favored : 93.77 % Rotamer: Outliers : 4.42 % Allowed : 26.82 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.23 (0.11), residues: 5646 helix: 0.99 (0.12), residues: 1871 sheet: -0.27 (0.16), residues: 1052 loop : -0.88 (0.12), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP c 214 HIS 0.009 0.001 HIS M 15 PHE 0.024 0.002 PHE E 54 TYR 0.055 0.002 TYR D 98 ARG 0.017 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1342 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1134 time to evaluate : 6.242 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: D 193 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7843 (mm110) REVERT: E 38 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.9079 (t) REVERT: E 83 ILE cc_start: 0.9220 (pp) cc_final: 0.8944 (pp) REVERT: E 88 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8468 (mm-30) REVERT: H 73 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7419 (tpt170) REVERT: K 62 ARG cc_start: 0.8792 (ptp-110) cc_final: 0.8299 (ttm-80) REVERT: K 70 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7681 (tp-100) REVERT: L 18 LYS cc_start: 0.8302 (tmtp) cc_final: 0.8100 (tmtm) REVERT: L 95 TYR cc_start: 0.8955 (m-80) cc_final: 0.8687 (m-80) REVERT: O 1 MET cc_start: 0.6401 (mmp) cc_final: 0.5954 (mmp) REVERT: O 60 GLN cc_start: 0.8691 (tp-100) cc_final: 0.7293 (tp40) REVERT: O 63 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7428 (mtm180) REVERT: O 80 ILE cc_start: 0.8949 (pp) cc_final: 0.8726 (pt) REVERT: Q 1 MET cc_start: 0.2569 (OUTLIER) cc_final: 0.1756 (ptp) REVERT: R 52 GLN cc_start: 0.8716 (tp40) cc_final: 0.8434 (tt0) REVERT: T 35 PHE cc_start: 0.9113 (t80) cc_final: 0.8834 (t80) REVERT: T 77 SER cc_start: 0.8686 (t) cc_final: 0.8461 (t) REVERT: G 4 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6700 (mtmm) REVERT: G 113 GLN cc_start: 0.8083 (tp40) cc_final: 0.7552 (tp40) REVERT: I 121 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.5856 (tmm) REVERT: J 143 LYS cc_start: 0.6961 (pptt) cc_final: 0.6723 (mptp) REVERT: J 147 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6488 (tt) REVERT: N 59 HIS cc_start: 0.7614 (t70) cc_final: 0.7369 (t70) REVERT: B 153 ARG cc_start: 0.6876 (mtp-110) cc_final: 0.6535 (tpt170) REVERT: B 154 ASP cc_start: 0.7691 (m-30) cc_final: 0.7169 (p0) REVERT: B 216 ARG cc_start: 0.5133 (mmm160) cc_final: 0.4854 (mmt-90) REVERT: c 101 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: c 134 ARG cc_start: 0.8661 (ptm-80) cc_final: 0.8367 (ptm-80) REVERT: c 148 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7577 (mtt180) REVERT: d 109 GLU cc_start: 0.7609 (tp30) cc_final: 0.7325 (tp30) REVERT: d 130 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.8909 (ptm160) REVERT: f 73 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9223 (ttpp) REVERT: f 87 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8472 (tmmt) REVERT: f 114 THR cc_start: 0.8997 (m) cc_final: 0.8749 (p) REVERT: f 184 PHE cc_start: 0.8391 (m-80) cc_final: 0.7634 (m-80) REVERT: i 80 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6901 (ptp-170) REVERT: i 129 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: i 141 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: l 111 GLU cc_start: 0.8057 (tp30) cc_final: 0.7804 (tp30) REVERT: m 43 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8514 (mtt-85) REVERT: n 24 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.7383 (ptp90) REVERT: n 28 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8634 (mtmt) REVERT: o 19 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7615 (tm-30) REVERT: o 63 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8598 (ttmm) REVERT: o 94 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.7862 (mtp85) REVERT: q 24 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8041 (tttp) REVERT: r 95 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: t 82 ASP cc_start: 0.7829 (p0) cc_final: 0.7237 (p0) REVERT: u 45 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8666 (mt) REVERT: x 70 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6628 (t0) REVERT: y 30 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8557 (mttm) REVERT: 0 11 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8902 (mtpt) REVERT: 0 45 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.8711 (ttp80) outliers start: 208 outliers final: 139 residues processed: 1236 average time/residue: 2.0695 time to fit residues: 3728.7376 Evaluate side-chains 1284 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1118 time to evaluate : 6.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain T residue 6 SER Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 63 SER Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain c residue 95 LEU Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain c residue 111 VAL Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain d residue 130 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain e residue 185 LEU Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 73 LYS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 138 THR Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 86 VAL Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain j residue 116 SER Chi-restraints excluded: chain k residue 21 VAL Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ASP Chi-restraints excluded: chain k residue 131 SER Chi-restraints excluded: chain l residue 54 MET Chi-restraints excluded: chain l residue 89 THR Chi-restraints excluded: chain l residue 113 VAL Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 24 ARG Chi-restraints excluded: chain n residue 28 LYS Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 44 SER Chi-restraints excluded: chain n residue 78 THR Chi-restraints excluded: chain o residue 7 GLU Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 5 VAL Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 24 LYS Chi-restraints excluded: chain q residue 36 THR Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain r residue 98 THR Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain t residue 33 ARG Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 95 VAL Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 60 SER Chi-restraints excluded: chain x residue 70 ASP Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 30 LYS Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain 0 residue 11 LYS Chi-restraints excluded: chain 0 residue 16 CYS Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 45 ARG Chi-restraints excluded: chain 1 residue 20 SER Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 38 SER Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 45 THR Chi-restraints excluded: chain 4 residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 596 optimal weight: 10.0000 chunk 961 optimal weight: 10.0000 chunk 586 optimal weight: 3.9990 chunk 455 optimal weight: 4.9990 chunk 668 optimal weight: 0.6980 chunk 1008 optimal weight: 40.0000 chunk 927 optimal weight: 10.0000 chunk 802 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 620 optimal weight: 9.9990 chunk 492 optimal weight: 0.7980 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 66 GLN ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN E 158 ASN E 168 GLN F 53 GLN L 5 GLN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN T 74 ASN I 41 ASN I 106 ASN J 117 GLN ** J 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN d 55 GLN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 ASN ** g 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 129 ASN ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 GLN l 67 ASN ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 GLN p 20 GLN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 ASN u 68 GLN y 19 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.433 156591 Z= 0.274 Angle : 0.739 69.523 234458 Z= 0.368 Chirality : 0.038 1.492 29802 Planarity : 0.006 0.130 12568 Dihedral : 23.906 179.891 79472 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.77 % Favored : 93.82 % Rotamer: Outliers : 3.70 % Allowed : 27.88 % Favored : 68.42 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.11), residues: 5646 helix: 0.96 (0.12), residues: 1870 sheet: -0.21 (0.16), residues: 1043 loop : -0.89 (0.12), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP c 214 HIS 0.008 0.001 HIS M 15 PHE 0.053 0.002 PHE P 105 TYR 0.032 0.002 TYR D 70 ARG 0.019 0.000 ARG K 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11292 Ramachandran restraints generated. 5646 Oldfield, 0 Emsley, 5646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1121 time to evaluate : 6.220 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: E 38 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9075 (t) REVERT: E 83 ILE cc_start: 0.9238 (pp) cc_final: 0.8963 (pp) REVERT: E 88 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8453 (mm-30) REVERT: F 3 LYS cc_start: 0.7724 (pmtt) cc_final: 0.7412 (ptpt) REVERT: H 73 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7462 (tpt170) REVERT: K 62 ARG cc_start: 0.8782 (ptp-110) cc_final: 0.8285 (ttm-80) REVERT: K 70 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7585 (tp-100) REVERT: L 18 LYS cc_start: 0.8299 (tmtp) cc_final: 0.7926 (tmtm) REVERT: L 95 TYR cc_start: 0.8956 (m-80) cc_final: 0.8687 (m-80) REVERT: O 1 MET cc_start: 0.6262 (mmp) cc_final: 0.5562 (mmp) REVERT: O 60 GLN cc_start: 0.8684 (tp-100) cc_final: 0.7285 (tp40) REVERT: O 63 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7409 (mtm180) REVERT: Q 1 MET cc_start: 0.2575 (OUTLIER) cc_final: 0.1758 (ptp) REVERT: R 52 GLN cc_start: 0.8708 (tp40) cc_final: 0.8438 (tt0) REVERT: T 35 PHE cc_start: 0.9086 (t80) cc_final: 0.8787 (t80) REVERT: T 77 SER cc_start: 0.8665 (t) cc_final: 0.8445 (t) REVERT: G 4 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6701 (mtmm) REVERT: G 113 GLN cc_start: 0.7990 (tp40) cc_final: 0.7396 (tp40) REVERT: I 121 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.5909 (tmm) REVERT: J 117 GLN cc_start: 0.5827 (OUTLIER) cc_final: 0.5605 (mt0) REVERT: J 147 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6458 (tt) REVERT: M 88 MET cc_start: 0.5312 (mtm) cc_final: 0.5043 (mtm) REVERT: N 59 HIS cc_start: 0.7610 (t70) cc_final: 0.7369 (t70) REVERT: B 153 ARG cc_start: 0.7011 (mtp-110) cc_final: 0.6669 (tpt170) REVERT: B 154 ASP cc_start: 0.7699 (m-30) cc_final: 0.7198 (p0) REVERT: B 216 ARG cc_start: 0.5082 (mmm160) cc_final: 0.4801 (mmt-90) REVERT: c 101 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: c 134 ARG cc_start: 0.8657 (ptm-80) cc_final: 0.8371 (ptm-80) REVERT: c 148 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7574 (mtt180) REVERT: d 87 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8344 (mt-10) REVERT: d 109 GLU cc_start: 0.7607 (tp30) cc_final: 0.7308 (tp30) REVERT: d 130 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.8914 (ptm160) REVERT: f 73 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.8739 (tppp) REVERT: f 87 LYS cc_start: 0.9283 (mtpp) cc_final: 0.8491 (tmmt) REVERT: f 114 THR cc_start: 0.8994 (m) cc_final: 0.8745 (p) REVERT: f 184 PHE cc_start: 0.8420 (m-80) cc_final: 0.7646 (m-80) REVERT: g 113 HIS cc_start: 0.8304 (p-80) cc_final: 0.8027 (p90) REVERT: i 80 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6813 (ptp-170) REVERT: i 129 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: i 141 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: j 105 GLU cc_start: 0.8906 (mp0) cc_final: 0.8520 (mp0) REVERT: l 111 GLU cc_start: 0.8064 (tp30) cc_final: 0.7825 (tp30) REVERT: m 43 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8499 (mtt-85) REVERT: n 24 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.7372 (ptp90) REVERT: o 19 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7610 (tm-30) REVERT: o 63 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8606 (ttmm) REVERT: o 94 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.7855 (mtp85) REVERT: q 24 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8020 (tttp) REVERT: r 95 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: t 82 ASP cc_start: 0.7791 (p0) cc_final: 0.7186 (p0) REVERT: u 45 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8654 (mt) REVERT: y 30 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8594 (mttm) REVERT: 0 11 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8915 (mtpt) REVERT: 0 45 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8707 (ttp80) outliers start: 174 outliers final: 128 residues processed: 1216 average time/residue: 2.0530 time to fit residues: 3636.9317 Evaluate side-chains 1258 residues out of total 4714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1104 time to evaluate : 6.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 133 TYR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 63 ARG Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 121 MET Chi-restraints excluded: chain J residue 117 GLN Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 160 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain c residue 95 LEU Chi-restraints excluded: chain c residue 101 GLU Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 184 MET Chi-restraints excluded: chain c residue 224 VAL Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 101 GLU Chi-restraints excluded: chain d residue 130 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 26 LEU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 183 ASP Chi-restraints excluded: chain f residue 58 VAL Chi-restraints excluded: chain f residue 69 ILE Chi-restraints excluded: chain f residue 73 LYS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain f residue 138 THR Chi-restraints excluded: chain g residue 52 LEU Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain i residue 80 ARG Chi-restraints excluded: chain i residue 86 VAL Chi-restraints excluded: chain i residue 129 GLU Chi-restraints excluded: chain i residue 141 GLU Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 65 THR Chi-restraints excluded: chain j residue 116 SER Chi-restraints excluded: chain k residue 21 VAL Chi-restraints excluded: chain k residue 63 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 122 ASP Chi-restraints excluded: chain k residue 131 SER Chi-restraints excluded: chain l residue 54 MET Chi-restraints excluded: chain l residue 89 THR Chi-restraints excluded: chain l residue 113 VAL Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain m residue 39 THR Chi-restraints excluded: chain m residue 43 ARG Chi-restraints excluded: chain m residue 57 THR Chi-restraints excluded: chain m residue 114 GLU Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 24 ARG Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 44 SER Chi-restraints excluded: chain n residue 78 THR Chi-restraints excluded: chain o residue 7 GLU Chi-restraints excluded: chain o residue 63 LYS Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 94 ARG Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 22 ILE Chi-restraints excluded: chain q residue 23 ASP Chi-restraints excluded: chain q residue 24 LYS Chi-restraints excluded: chain q residue 36 THR Chi-restraints excluded: chain q residue 51 ASP Chi-restraints excluded: chain q residue 56 VAL Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 41 VAL Chi-restraints excluded: chain r residue 95 GLU Chi-restraints excluded: chain r residue 98 THR Chi-restraints excluded: chain r residue 109 SER Chi-restraints excluded: chain s residue 58 SER Chi-restraints excluded: chain t residue 33 ARG Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 37 ASP Chi-restraints excluded: chain u residue 45 LEU Chi-restraints excluded: chain u residue 95 VAL Chi-restraints excluded: chain u residue 96 ARG Chi-restraints excluded: chain v residue 38 VAL Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 59 VAL Chi-restraints excluded: chain w residue 60 SER Chi-restraints excluded: chain y residue 8 THR Chi-restraints excluded: chain y residue 30 LYS Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain 0 residue 11 LYS Chi-restraints excluded: chain 0 residue 16 CYS Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 45 ARG Chi-restraints excluded: chain 1 residue 20 SER Chi-restraints excluded: chain 1 residue 23 SER Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 38 SER Chi-restraints excluded: chain 4 residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 637 optimal weight: 5.9990 chunk 855 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 740 optimal weight: 20.0000 chunk 118 optimal weight: 40.0000 chunk 223 optimal weight: 8.9990 chunk 804 optimal weight: 8.9990 chunk 336 optimal weight: 20.0000 chunk 825 optimal weight: 10.0000 chunk 101 optimal weight: 40.0000 chunk 148 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN D 66 GLN ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN E 158 ASN E 168 GLN F 53 GLN H 16 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN T 74 ASN ** P 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 HIS I 41 ASN I 106 ASN ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 GLN ** J 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 212 ASN d 25 ASN ** f 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 34 ASN ** g 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 129 ASN ** g 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 GLN l 67 ASN ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 GLN p 20 GLN ** r 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 GLN x 64 ASN y 19 ASN z 19 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.059480 restraints weight = 449579.922| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 1.46 r_work: 0.2564 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2468 r_free = 0.2468 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.433 156591 Z= 0.504 Angle : 0.823 69.348 234458 Z= 0.409 Chirality : 0.046 1.475 29802 Planarity : 0.007 0.141 12568 Dihedral : 23.908 179.685 79472 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.41 % Favored : 93.16 % Rotamer: Outliers : 4.16 % Allowed : 27.33 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.43 (0.11), residues: 5646 helix: 0.77 (0.12), residues: 1879 sheet: -0.35 (0.16), residues: 1054 loop : -0.97 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 214 HIS 0.010 0.001 HIS K 124 PHE 0.023 0.002 PHE U 10 TYR 0.033 0.002 TYR D 70 ARG 0.018 0.001 ARG K 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54425.58 seconds wall clock time: 942 minutes 38.93 seconds (56558.93 seconds total)