Starting phenix.real_space_refine on Tue Feb 20 13:28:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvw_26818/02_2024/7uvw_26818_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvw_26818/02_2024/7uvw_26818.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvw_26818/02_2024/7uvw_26818_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvw_26818/02_2024/7uvw_26818_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvw_26818/02_2024/7uvw_26818_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvw_26818/02_2024/7uvw_26818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvw_26818/02_2024/7uvw_26818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvw_26818/02_2024/7uvw_26818_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvw_26818/02_2024/7uvw_26818_updated.pdb" } resolution = 2.37 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= 0.005 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4440 5.49 5 S 142 5.16 5 C 69371 2.51 5 N 25707 2.21 5 O 38572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 3": "OD1" <-> "OD2" Residue "0 TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 31": "OE1" <-> "OE2" Residue "0 ASP 36": "OD1" <-> "OD2" Residue "2 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 53": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ASP 153": "OD1" <-> "OD2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 2": "OD1" <-> "OD2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I ASP 14": "OD1" <-> "OD2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "J ASP 80": "OD1" <-> "OD2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 105": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q ASP 45": "OD1" <-> "OD2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R ASP 94": "OD1" <-> "OD2" Residue "S TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "S PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 78": "OD1" <-> "OD2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "T ASP 8": "OD1" <-> "OD2" Residue "T GLU 29": "OE1" <-> "OE2" Residue "T ASP 30": "OD1" <-> "OD2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "U ASP 14": "OD1" <-> "OD2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U GLU 50": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 15": "OD1" <-> "OD2" Residue "V PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 70": "OE1" <-> "OE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "W GLU 43": "OE1" <-> "OE2" Residue "X GLU 13": "OE1" <-> "OE2" Residue "X ASP 19": "OD1" <-> "OD2" Residue "Y TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 14": "OD1" <-> "OD2" Residue "Z ASP 20": "OD1" <-> "OD2" Residue "b ASP 118": "OD1" <-> "OD2" Residue "b PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 135": "OE1" <-> "OE2" Residue "c TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c ASP 107": "OD1" <-> "OD2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 181": "OD1" <-> "OD2" Residue "c ASP 183": "OD1" <-> "OD2" Residue "c GLU 190": "OE1" <-> "OE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d GLU 15": "OE1" <-> "OE2" Residue "d PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d GLU 90": "OE1" <-> "OE2" Residue "d PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 149": "OE1" <-> "OE2" Residue "d GLU 174": "OE1" <-> "OE2" Residue "d GLU 181": "OE1" <-> "OE2" Residue "d TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 40": "OD1" <-> "OD2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e ASP 74": "OD1" <-> "OD2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 150": "OE1" <-> "OE2" Residue "e GLU 161": "OE1" <-> "OE2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "g ASP 33": "OD1" <-> "OD2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "g GLU 139": "OE1" <-> "OE2" Residue "h ASP 9": "OD1" <-> "OD2" Residue "h GLU 50": "OE1" <-> "OE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 91": "OD1" <-> "OD2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "i PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m ASP 11": "OD1" <-> "OD2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m ASP 49": "OD1" <-> "OD2" Residue "m GLU 72": "OE1" <-> "OE2" Residue "m ASP 82": "OD1" <-> "OD2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 92": "OD1" <-> "OD2" Residue "o ASP 38": "OD1" <-> "OD2" Residue "o ASP 74": "OD1" <-> "OD2" Residue "o GLU 76": "OE1" <-> "OE2" Residue "p ASP 41": "OD1" <-> "OD2" Residue "p PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p ASP 73": "OD1" <-> "OD2" Residue "p PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 19": "OD1" <-> "OD2" Residue "q GLU 27": "OE1" <-> "OE2" Residue "q ASP 49": "OD1" <-> "OD2" Residue "q GLU 64": "OE1" <-> "OE2" Residue "r ASP 22": "OD1" <-> "OD2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s ASP 43": "OD1" <-> "OD2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "t TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 63": "OD1" <-> "OD2" Residue "u TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 138233 Number of models: 1 Model: "" Number of chains: 54 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 58332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2719, 58332 Classifications: {'RNA': 2719} Modifications used: {'rna2p': 3, 'rna2p_pur': 261, 'rna2p_pyr': 156, 'rna3p': 9, 'rna3p_pur': 1293, 'rna3p_pyr': 997} Link IDs: {'rna2p': 419, 'rna3p': 2299} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1516 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 873 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "O" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "T" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Y" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 455 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "Z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "a" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 114, 'rna2p_pyr': 90, 'rna3p': 8, 'rna3p_pur': 749, 'rna3p_pyr': 566} Link IDs: {'rna2p': 204, 'rna3p': 1323} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1073 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "v" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1636 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p': 2, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 2, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 47.232 111.086 140.904 1.00 64.21 S ATOM 1398 SG CYS 3 14 47.838 112.402 137.394 1.00 62.28 S ATOM 1503 SG CYS 3 27 46.080 114.569 139.979 1.00 62.14 S Time building chain proxies: 52.84, per 1000 atoms: 0.38 Number of scatterers: 138233 At special positions: 0 Unit cell: (228.112, 241.68, 274.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 142 16.00 P 4440 15.00 O 38572 8.00 N 25707 7.00 C 69371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 52.65 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " Number of angles added : 3 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10106 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 179 helices and 68 sheets defined 40.1% alpha, 19.7% beta 1503 base pairs and 2299 stacking pairs defined. Time for finding SS restraints: 70.12 Creating SS restraints... Processing helix chain '0' and resid 22 through 27 Proline residue: 0 27 - end of helix Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.146A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.538A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 36 removed outlier: 4.818A pdb=" N LYS 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER 2 36 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 31 through 36' Processing helix chain '2' and resid 37 through 45 removed outlier: 3.983A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.491A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 15 removed outlier: 4.957A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.843A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.901A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.030A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 265 removed outlier: 4.953A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 265' Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.255A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.649A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.588A pdb=" N GLU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.987A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.446A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.658A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.642A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.723A pdb=" N PHE E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 4 through 11 removed outlier: 4.043A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 21 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.780A pdb=" N ILE F 28 " --> pdb=" O ASN F 24 " (cutoff:3.500A) Proline residue: F 29 - end of helix No H-bonds generated for 'chain 'F' and resid 24 through 29' Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.347A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 4.744A pdb=" N GLY F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.147A pdb=" N ILE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 4.514A pdb=" N ILE F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASP F 147 " --> pdb=" O PHE F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.879A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.754A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 3.697A pdb=" N ARG H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.699A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 4.224A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.721A pdb=" N PHE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 3.550A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 removed outlier: 4.302A pdb=" N ILE J 115 " --> pdb=" O PHE J 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.870A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.768A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 4.281A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 85 removed outlier: 4.006A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 85' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.918A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 4.029A 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 37 through 57 removed outlier: 3.870A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 3.624A pdb=" N LYS M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.881A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 2 through 23 removed outlier: 4.490A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 16 removed outlier: 3.720A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.787A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 107' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.721A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.873A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.625A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.945A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 103 through 118 Processing helix chain 'R' and resid 13 through 25 removed outlier: 4.044A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.195A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 4.239A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.431A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.206A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 3.736A pdb=" N GLN U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 12 through 17' Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 57 removed outlier: 4.230A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 63 removed outlier: 4.584A pdb=" N GLU U 62 " --> pdb=" O ASN U 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 removed outlier: 3.647A pdb=" N GLY W 75 " --> pdb=" O LEU W 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 10 removed outlier: 3.732A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 removed outlier: 3.586A pdb=" N ASP X 19 " --> pdb=" O LYS X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 61 removed outlier: 3.793A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA X 51 " --> pdb=" O ARG X 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.642A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 4.954A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 15 Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.084A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 4.202A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 76 through 90 removed outlier: 4.696A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 106 removed outlier: 3.592A pdb=" N TRP b 106 " --> pdb=" O MET b 102 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 126 removed outlier: 4.396A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 3.637A pdb=" N LEU b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N THR b 132 " --> pdb=" O PHE b 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 127 through 132' Processing helix chain 'b' and resid 133 through 151 Processing helix chain 'b' and resid 167 through 172 Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 227 removed outlier: 4.240A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.613A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 4.852A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.621A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.651A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 3.976A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 removed outlier: 3.757A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 5.108A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 removed outlier: 3.534A pdb=" N VAL d 63 " --> pdb=" O GLU d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.073A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.751A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 108 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 148 through 153 removed outlier: 5.614A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 4.431A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 Proline residue: d 194 - end of helix Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.106A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.280A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.582A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 11 through 19 removed outlier: 4.809A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 33 Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 32 removed outlier: 5.744A pdb=" N GLN g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.795A pdb=" N LYS g 55 " --> pdb=" O GLN g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.662A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA g 108 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.842A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.766A pdb=" N ALA g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (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 113 through 121 Processing helix chain 'i' and resid 32 through 37 Processing helix chain 'i' and resid 39 through 54 removed outlier: 3.779A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.615A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 100 Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.873A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.554A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 58 through 77 removed outlier: 3.678A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.016A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.775A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.056A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.984A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASP m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.868A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 21 Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.562A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.599A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN n 90 " --> pdb=" O ASP n 86 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY n 91 " --> pdb=" O THR n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 57 Proline residue: n 57 - end of helix Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.505A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.957A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 71 through 82 Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.771A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.711A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 70 through 76 removed outlier: 4.650A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 3.733A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 38 removed outlier: 4.445A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TYR u 38 " --> pdb=" O LYS u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '0' and resid 15 through 21 removed outlier: 5.933A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 1 through 5 removed outlier: 6.765A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.265A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.898A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.086A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 179 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG C 271 " --> pdb=" O GLY C 179 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 269 " --> pdb=" O MET C 181 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.292A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.468A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 80 through 85 removed outlier: 4.885A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 11, first strand: chain 'D' and resid 25 through 30 removed outlier: 5.385A pdb=" N SER D 188 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 108 through 111 removed outlier: 4.516A pdb=" N GLN D 108 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.830A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 43 through 46 removed outlier: 7.029A pdb=" N ARG E 43 " --> pdb=" O PRO E 88 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA E 86 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 116 through 119 removed outlier: 5.620A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.721A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 18, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 19, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.339A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 21, first strand: chain 'H' and resid 16 through 20 removed outlier: 4.358A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 6 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.961A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.542A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.213A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.633A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE L 34 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS L 101 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 31 through 37 removed outlier: 8.065A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 33 through 36 removed outlier: 5.006A pdb=" N ARG M 103 " --> pdb=" O ALA M 107 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL M 113 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL M 97 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU M 115 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 50 through 53 Processing sheet with id= 29, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.783A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 52 through 56 removed outlier: 3.896A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG O 56 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 11 through 15 removed outlier: 3.958A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN Q 46 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.220A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 34, first strand: chain 'Q' and resid 65 through 72 removed outlier: 3.762A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 36, first strand: chain 'S' and resid 27 through 32 removed outlier: 6.118A pdb=" N GLY S 27 " --> pdb=" O LEU S 86 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 38 through 43 removed outlier: 5.541A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 81 through 85 Processing sheet with id= 39, first strand: chain 'U' and resid 73 through 76 removed outlier: 3.536A pdb=" N ALA U 93 " --> pdb=" O PRO U 31 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.581A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 29 through 32 removed outlier: 4.635A pdb=" N GLN V 29 " --> pdb=" O VAL V 67 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.296A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.381A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 45, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.187A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'b' and resid 17 through 20 removed outlier: 4.830A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 92 through 95 Processing sheet with id= 48, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.811A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.603A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 142 through 146 removed outlier: 3.728A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N TRP d 172 " --> pdb=" O LYS d 185 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 10 through 15 removed outlier: 6.794A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.778A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 32 through 40 removed outlier: 6.798A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 38 through 42 removed outlier: 6.100A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.949A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.655A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.637A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'i' and resid 3 through 9 removed outlier: 4.086A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 35 through 38 removed outlier: 3.561A pdb=" N GLN j 35 " --> pdb=" O VAL j 77 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.670A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 62, first strand: chain 'k' and resid 29 through 34 removed outlier: 7.080A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 29 through 33 removed outlier: 5.209A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.955A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.528A pdb=" N PHE p 34 " --> pdb=" O GLY p 27 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 7 through 12 removed outlier: 5.881A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 's' and resid 30 through 34 removed outlier: 4.413A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASN s 56 " --> pdb=" O ASN s 53 " (cutoff:3.500A) 1892 hydrogen bonds defined for protein. 5601 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3755 hydrogen bonds 5856 hydrogen bond angles 0 basepair planarities 1503 basepair parallelities 2299 stacking parallelities Total time for adding SS restraints: 241.40 Time building geometry restraints manager: 57.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 12988 1.31 - 1.43: 66833 1.43 - 1.56: 61261 1.56 - 1.69: 8874 1.69 - 1.82: 253 Bond restraints: 150209 Sorted by residual: bond pdb=" C4 5MU A1935 " pdb=" C5 5MU A1935 " ideal model delta sigma weight residual 1.802 1.445 0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" C4 5MU v 55 " pdb=" C5 5MU v 55 " ideal model delta sigma weight residual 1.802 1.449 0.353 2.00e-02 2.50e+03 3.12e+02 bond pdb=" N1 5MU A1935 " pdb=" C6 5MU A1935 " ideal model delta sigma weight residual 1.635 1.369 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" N1 5MU v 55 " pdb=" C6 5MU v 55 " ideal model delta sigma weight residual 1.635 1.377 0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" N3 5MU v 55 " pdb=" C4 5MU v 55 " ideal model delta sigma weight residual 1.182 1.383 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 150204 not shown) Histogram of bond angle deviations from ideal: 97.20 - 107.17: 27845 107.17 - 117.15: 108917 117.15 - 127.12: 77598 127.12 - 137.09: 10422 137.09 - 147.06: 3 Bond angle restraints: 224785 Sorted by residual: angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 147.06 -20.83 3.00e+00 1.11e-01 4.82e+01 angle pdb=" C1' OMG A2247 " pdb=" N9 OMG A2247 " pdb=" C4 OMG A2247 " ideal model delta sigma weight residual 108.29 127.27 -18.98 3.00e+00 1.11e-01 4.00e+01 angle pdb=" C1' 2MG a1204 " pdb=" N9 2MG a1204 " pdb=" C8 2MG a1204 " ideal model delta sigma weight residual 110.07 128.53 -18.46 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C1' 2MG a 963 " pdb=" N9 2MG a 963 " pdb=" C8 2MG a 963 " ideal model delta sigma weight residual 110.07 127.76 -17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" C6 5MU v 55 " pdb=" C5 5MU v 55 " pdb=" C5M 5MU v 55 " ideal model delta sigma weight residual 106.09 123.63 -17.54 3.00e+00 1.11e-01 3.42e+01 ... (remaining 224780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 84977 35.95 - 71.90: 9801 71.90 - 107.84: 1105 107.84 - 143.79: 24 143.79 - 179.74: 63 Dihedral angle restraints: 95970 sinusoidal: 80281 harmonic: 15689 Sorted by residual: dihedral pdb=" C4' U A2502 " pdb=" C3' U A2502 " pdb=" C2' U A2502 " pdb=" C1' U A2502 " ideal model delta sinusoidal sigma weight residual -35.00 34.45 -69.45 1 8.00e+00 1.56e-02 9.74e+01 dihedral pdb=" C5' U A2502 " pdb=" C4' U A2502 " pdb=" C3' U A2502 " pdb=" O3' U A2502 " ideal model delta sinusoidal sigma weight residual 147.00 79.56 67.44 1 8.00e+00 1.56e-02 9.24e+01 dihedral pdb=" O4' C a1448 " pdb=" C1' C a1448 " pdb=" N1 C a1448 " pdb=" C2 C a1448 " ideal model delta sinusoidal sigma weight residual -160.00 19.05 -179.05 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 95967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 26839 0.072 - 0.145: 1727 0.145 - 0.217: 135 0.217 - 0.289: 25 0.289 - 0.362: 6 Chirality restraints: 28732 Sorted by residual: chirality pdb=" C3' U A2502 " pdb=" C4' U A2502 " pdb=" O3' U A2502 " pdb=" C2' U A2502 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" C1* PSU A2576 " pdb=" O4* PSU A2576 " pdb=" C2* PSU A2576 " pdb=" C5 PSU A2576 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA ARG b 139 " pdb=" N ARG b 139 " pdb=" C ARG b 139 " pdb=" CB ARG b 139 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 28729 not shown) Planarity restraints: 12006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " -0.066 2.00e-02 2.50e+03 6.15e-01 8.52e+03 pdb=" C4' 7MG A2065 " -0.449 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " -0.685 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " 0.650 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " 0.182 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " -0.982 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " -0.205 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " 0.956 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2441 " 0.025 2.00e-02 2.50e+03 5.88e-01 7.77e+03 pdb=" C4' 2MG A2441 " 0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG A2441 " 0.721 2.00e-02 2.50e+03 pdb=" C3' 2MG A2441 " -0.591 2.00e-02 2.50e+03 pdb=" O3' 2MG A2441 " -0.564 2.00e-02 2.50e+03 pdb=" C2' 2MG A2441 " -0.225 2.00e-02 2.50e+03 pdb=" O2' 2MG A2441 " 0.892 2.00e-02 2.50e+03 pdb=" C1' 2MG A2441 " 0.210 2.00e-02 2.50e+03 pdb=" N9 2MG A2441 " -0.912 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.055 2.00e-02 2.50e+03 5.78e-01 7.51e+03 pdb=" C4' 2MG a1204 " 0.427 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.595 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.596 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.602 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.948 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.232 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.871 2.00e-02 2.50e+03 ... (remaining 12003 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 4471 2.65 - 3.21: 108291 3.21 - 3.78: 265010 3.78 - 4.34: 368165 4.34 - 4.90: 483210 Nonbonded interactions: 1229147 Sorted by model distance: nonbonded pdb=" OG1 THR i 56 " pdb=" OE1 GLU i 57 " model vdw 2.091 2.440 nonbonded pdb=" O2' C A1412 " pdb=" O2' G A1585 " model vdw 2.107 2.440 nonbonded pdb=" O2' U A 533 " pdb=" OD2 ASP P 49 " model vdw 2.115 2.440 nonbonded pdb=" OD1 ASP O 39 " pdb=" NH2 ARG O 40 " model vdw 2.122 2.520 nonbonded pdb=" O2' A A2804 " pdb=" O6 G A2886 " model vdw 2.123 2.440 ... (remaining 1229142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.570 Construct map_model_manager: 0.080 Extract box with map and model: 30.230 Check model and map are aligned: 1.490 Set scattering table: 0.920 Process input model: 537.350 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.390 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 593.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.357 150209 Z= 0.290 Angle : 0.647 20.829 224785 Z= 0.340 Chirality : 0.038 0.362 28732 Planarity : 0.017 0.615 12006 Dihedral : 23.088 179.740 85864 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.64 % Favored : 97.23 % Rotamer: Outliers : 2.30 % Allowed : 25.69 % Favored : 72.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.61 (0.11), residues: 5414 helix: 1.67 (0.12), residues: 1855 sheet: 0.50 (0.16), residues: 1060 loop : -0.58 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 62 HIS 0.008 0.001 HIS C 25 PHE 0.017 0.002 PHE M 102 TYR 0.015 0.001 TYR P 32 ARG 0.025 0.001 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1047 time to evaluate : 5.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 ARG cc_start: 0.7540 (ttp80) cc_final: 0.6603 (ttp80) REVERT: F 57 MET cc_start: 0.7067 (mtp) cc_final: 0.6612 (mtp) REVERT: F 177 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6110 (t80) REVERT: W 45 ARG cc_start: 0.8332 (ptt90) cc_final: 0.8064 (ptt90) REVERT: b 80 ASN cc_start: 0.5097 (t0) cc_final: 0.4536 (t0) REVERT: b 107 LYS cc_start: 0.7933 (mtpt) cc_final: 0.7730 (mttp) REVERT: b 148 ARG cc_start: 0.6026 (mtp85) cc_final: 0.5312 (mtp85) REVERT: d 118 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: j 28 THR cc_start: 0.8756 (m) cc_final: 0.8477 (m) outliers start: 103 outliers final: 69 residues processed: 1129 average time/residue: 2.1586 time to fit residues: 3414.4224 Evaluate side-chains 1079 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1008 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 44 VAL Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 177 PHE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 65 SER Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 32 ASN Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 0.9990 chunk 736 optimal weight: 0.8980 chunk 408 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 496 optimal weight: 6.9990 chunk 393 optimal weight: 4.9990 chunk 761 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 463 optimal weight: 6.9990 chunk 567 optimal weight: 20.0000 chunk 882 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 120 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN N 51 GLN O 9 GLN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 24 GLN Y 38 GLN Y 48 ASN ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 25 ASN c 28 GLN c 88 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 23 GLN h 42 GLN h 86 GLN j 99 GLN o 40 GLN q 31 GLN r 31 GLN s 65 HIS t 3 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.0407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 150209 Z= 0.235 Angle : 0.626 15.698 224785 Z= 0.339 Chirality : 0.038 0.353 28732 Planarity : 0.006 0.132 12006 Dihedral : 23.014 179.891 75224 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.73 % Favored : 97.12 % Rotamer: Outliers : 4.08 % Allowed : 22.85 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.78 (0.11), residues: 5414 helix: 1.88 (0.12), residues: 1862 sheet: 0.57 (0.16), residues: 1060 loop : -0.53 (0.11), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 201 HIS 0.008 0.001 HIS C 25 PHE 0.014 0.001 PHE D 121 TYR 0.015 0.001 TYR P 32 ARG 0.011 0.000 ARG c 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1041 time to evaluate : 5.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 57 MET cc_start: 0.7038 (mtp) cc_final: 0.6606 (mtp) REVERT: G 69 ARG cc_start: 0.8929 (tmt170) cc_final: 0.8697 (tpt90) REVERT: G 99 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7811 (ttpt) REVERT: I 61 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: I 79 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: J 53 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8132 (mmtm) REVERT: M 30 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: R 2 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: Z 38 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7674 (ttt180) REVERT: b 34 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7196 (t80) REVERT: b 80 ASN cc_start: 0.4883 (t0) cc_final: 0.4423 (t0) REVERT: b 109 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7498 (mm) REVERT: f 76 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8023 (tp30) REVERT: g 138 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7669 (tpt-90) REVERT: g 144 MET cc_start: 0.7301 (mmt) cc_final: 0.7100 (mmt) REVERT: l 88 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7690 (tptm) REVERT: s 32 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8638 (ttmm) REVERT: t 18 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8442 (ttm170) outliers start: 183 outliers final: 88 residues processed: 1134 average time/residue: 2.1929 time to fit residues: 3470.4273 Evaluate side-chains 1112 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1010 time to evaluate : 5.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 0 residue 46 LYS Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 30 GLU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain X residue 61 GLN Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 ARG Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain b residue 37 ARG Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 179 LYS Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 76 GLU Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 138 ARG Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 32 ASN Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain n residue 86 ASP Chi-restraints excluded: chain q residue 38 SER Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 36 LEU Chi-restraints excluded: chain t residue 37 SER Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 490 optimal weight: 7.9990 chunk 273 optimal weight: 8.9990 chunk 734 optimal weight: 8.9990 chunk 601 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 884 optimal weight: 9.9990 chunk 955 optimal weight: 0.7980 chunk 787 optimal weight: 8.9990 chunk 876 optimal weight: 5.9990 chunk 301 optimal weight: 0.8980 chunk 709 optimal weight: 10.0000 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 120 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN O 9 GLN Q 43 ASN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN Y 48 ASN b 60 ASN ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 88 GLN d 118 GLN d 166 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 23 GLN h 42 GLN h 86 GLN j 99 GLN o 40 GLN q 31 GLN r 31 GLN r 54 GLN s 57 HIS s 65 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 150209 Z= 0.369 Angle : 0.691 14.295 224785 Z= 0.369 Chirality : 0.042 0.351 28732 Planarity : 0.006 0.142 12006 Dihedral : 22.980 179.772 75172 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.08 % Favored : 96.77 % Rotamer: Outliers : 4.86 % Allowed : 22.16 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 5414 helix: 1.75 (0.12), residues: 1870 sheet: 0.53 (0.16), residues: 1056 loop : -0.63 (0.11), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 201 HIS 0.009 0.001 HIS C 25 PHE 0.021 0.002 PHE D 121 TYR 0.019 0.002 TYR P 32 ARG 0.012 0.001 ARG c 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1032 time to evaluate : 5.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 47 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: 3 15 LYS cc_start: 0.8259 (ttmm) cc_final: 0.7935 (ttpt) REVERT: E 120 VAL cc_start: 0.8991 (OUTLIER) cc_final: 0.8707 (m) REVERT: E 134 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8924 (tt) REVERT: F 57 MET cc_start: 0.7077 (mtp) cc_final: 0.6587 (mtp) REVERT: G 99 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7789 (ttpt) REVERT: I 61 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: I 79 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: J 53 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8028 (mmtm) REVERT: O 47 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: R 2 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: W 45 ARG cc_start: 0.8297 (ptt90) cc_final: 0.8027 (ptt90) REVERT: Z 38 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7721 (ttt180) REVERT: b 34 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7205 (t80) REVERT: b 80 ASN cc_start: 0.4797 (t0) cc_final: 0.4323 (t0) REVERT: b 109 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7551 (mm) REVERT: b 191 THR cc_start: 0.7014 (OUTLIER) cc_final: 0.6713 (t) REVERT: f 31 GLU cc_start: 0.8884 (pp20) cc_final: 0.8677 (pp20) REVERT: g 114 LYS cc_start: 0.7871 (mttp) cc_final: 0.7607 (mttp) REVERT: g 144 MET cc_start: 0.7439 (mmt) cc_final: 0.7132 (mmt) REVERT: i 57 GLU cc_start: 0.8100 (mp0) cc_final: 0.7864 (mp0) REVERT: l 88 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7705 (tptm) REVERT: o 44 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8157 (mtpt) REVERT: s 32 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8505 (tttm) REVERT: t 18 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8498 (ttm170) outliers start: 218 outliers final: 115 residues processed: 1158 average time/residue: 2.1750 time to fit residues: 3525.9289 Evaluate side-chains 1138 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1006 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 0 residue 46 LYS Chi-restraints excluded: chain 0 residue 47 GLU Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 ARG Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 179 LYS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 137 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 23 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 32 ASN Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain n residue 86 ASP Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 38 SER Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 36 LEU Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 873 optimal weight: 10.0000 chunk 664 optimal weight: 7.9990 chunk 458 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 422 optimal weight: 3.9990 chunk 593 optimal weight: 7.9990 chunk 887 optimal weight: 4.9990 chunk 939 optimal weight: 4.9990 chunk 463 optimal weight: 0.8980 chunk 841 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 120 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN Q 43 ASN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 24 GLN Y 38 GLN ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 88 GLN d 118 GLN f 58 HIS h 23 GLN h 42 GLN h 86 GLN j 99 GLN o 40 GLN q 31 GLN r 31 GLN r 54 GLN s 65 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 150209 Z= 0.301 Angle : 0.660 14.708 224785 Z= 0.356 Chirality : 0.040 0.352 28732 Planarity : 0.006 0.161 12006 Dihedral : 22.976 179.935 75169 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.96 % Favored : 96.88 % Rotamer: Outliers : 4.68 % Allowed : 22.81 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.67 (0.11), residues: 5414 helix: 1.80 (0.12), residues: 1869 sheet: 0.55 (0.16), residues: 1054 loop : -0.64 (0.11), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 103 HIS 0.008 0.001 HIS C 25 PHE 0.018 0.002 PHE D 121 TYR 0.017 0.002 TYR P 32 ARG 0.013 0.000 ARG J 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1033 time to evaluate : 5.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 47 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: 1 1 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7638 (mtp) REVERT: 3 15 LYS cc_start: 0.8265 (ttmm) cc_final: 0.7955 (ttpt) REVERT: E 120 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8726 (m) REVERT: F 20 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7996 (mm) REVERT: F 57 MET cc_start: 0.7131 (mtp) cc_final: 0.6683 (mtp) REVERT: G 99 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7781 (ttpt) REVERT: I 61 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: I 79 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: J 53 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8071 (mmtm) REVERT: N 87 THR cc_start: 0.8909 (p) cc_final: 0.8703 (p) REVERT: R 2 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: S 1 MET cc_start: 0.3413 (OUTLIER) cc_final: 0.2982 (ptt) REVERT: W 45 ARG cc_start: 0.8298 (ptt90) cc_final: 0.8012 (ptt90) REVERT: W 72 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8497 (mtt-85) REVERT: Z 38 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7723 (ttt180) REVERT: b 34 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7193 (t80) REVERT: b 80 ASN cc_start: 0.4988 (t0) cc_final: 0.4550 (t0) REVERT: c 72 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8194 (mtt-85) REVERT: e 61 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8706 (mttp) REVERT: f 21 MET cc_start: 0.7764 (mtp) cc_final: 0.7511 (mtt) REVERT: f 31 GLU cc_start: 0.8923 (pp20) cc_final: 0.8695 (pp20) REVERT: f 76 GLU cc_start: 0.8449 (tp30) cc_final: 0.8127 (tp30) REVERT: g 114 LYS cc_start: 0.7863 (mttp) cc_final: 0.7596 (mttp) REVERT: g 144 MET cc_start: 0.7444 (mmt) cc_final: 0.7119 (mmt) REVERT: i 57 GLU cc_start: 0.8099 (mp0) cc_final: 0.7837 (mp0) REVERT: i 128 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6518 (mtm-85) REVERT: l 88 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7712 (tptm) REVERT: o 44 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8115 (mtpt) REVERT: s 32 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8497 (tttm) REVERT: u 63 GLU cc_start: 0.0008 (OUTLIER) cc_final: -0.1238 (mp0) outliers start: 210 outliers final: 127 residues processed: 1149 average time/residue: 2.1768 time to fit residues: 3502.6321 Evaluate side-chains 1157 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1010 time to evaluate : 5.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 0 residue 46 LYS Chi-restraints excluded: chain 0 residue 47 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 35 GLU Chi-restraints excluded: chain Z residue 38 ARG Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 110 ARG Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 163 LEU Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 179 LYS Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 137 ASN Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 23 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 SER Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 32 ASN Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 86 ASP Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 38 SER Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 36 LEU Chi-restraints excluded: chain t residue 37 SER Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 782 optimal weight: 20.0000 chunk 533 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 699 optimal weight: 30.0000 chunk 387 optimal weight: 7.9990 chunk 801 optimal weight: 10.0000 chunk 649 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 479 optimal weight: 10.0000 chunk 843 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 120 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN O 9 GLN Q 43 ASN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 24 GLN Y 38 GLN b 60 ASN ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 88 GLN d 118 GLN f 58 HIS h 23 GLN h 86 GLN j 99 GLN o 40 GLN q 31 GLN r 31 GLN r 54 GLN s 65 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 150209 Z= 0.486 Angle : 0.757 15.415 224785 Z= 0.398 Chirality : 0.046 0.390 28732 Planarity : 0.007 0.145 12006 Dihedral : 22.995 179.355 75169 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.42 % Favored : 96.44 % Rotamer: Outliers : 5.26 % Allowed : 22.54 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.48 (0.11), residues: 5414 helix: 1.60 (0.12), residues: 1870 sheet: 0.50 (0.16), residues: 1043 loop : -0.74 (0.11), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 201 HIS 0.019 0.002 HIS f 58 PHE 0.026 0.002 PHE D 121 TYR 0.021 0.002 TYR P 32 ARG 0.014 0.001 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1021 time to evaluate : 5.897 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: 0 47 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: 1 1 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7680 (mtp) REVERT: C 175 ARG cc_start: 0.7366 (ttp80) cc_final: 0.7048 (ttp80) REVERT: C 200 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8229 (t0) REVERT: E 120 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8724 (m) REVERT: F 20 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7917 (mm) REVERT: F 57 MET cc_start: 0.7179 (mtp) cc_final: 0.6740 (mtp) REVERT: G 99 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7789 (ttpt) REVERT: I 61 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: I 79 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: J 53 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8131 (mmpt) REVERT: J 86 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9048 (mm) REVERT: J 97 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6279 (mtp180) REVERT: L 6 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7371 (mtp85) REVERT: R 2 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: S 1 MET cc_start: 0.3309 (OUTLIER) cc_final: 0.2905 (ptt) REVERT: W 72 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8517 (mtt-85) REVERT: X 47 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8650 (ttt90) REVERT: Z 38 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7774 (ttt180) REVERT: b 34 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7175 (t80) REVERT: b 80 ASN cc_start: 0.4970 (t0) cc_final: 0.4527 (t0) REVERT: b 169 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7812 (p0) REVERT: b 191 THR cc_start: 0.7097 (OUTLIER) cc_final: 0.6798 (t) REVERT: c 72 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8329 (mtt-85) REVERT: e 61 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8699 (mttp) REVERT: f 21 MET cc_start: 0.7811 (mtp) cc_final: 0.7541 (mtt) REVERT: f 31 GLU cc_start: 0.8911 (pp20) cc_final: 0.8648 (pp20) REVERT: f 58 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8088 (m-70) REVERT: g 144 MET cc_start: 0.7489 (mmt) cc_final: 0.7137 (mmt) REVERT: i 57 GLU cc_start: 0.8100 (mp0) cc_final: 0.7843 (mp0) REVERT: i 128 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6518 (mtm-85) REVERT: l 88 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7723 (tptm) REVERT: s 32 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8520 (tttm) REVERT: t 18 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8495 (ttm170) REVERT: u 63 GLU cc_start: 0.0067 (OUTLIER) cc_final: -0.1035 (mp0) outliers start: 236 outliers final: 139 residues processed: 1156 average time/residue: 2.1906 time to fit residues: 3555.0839 Evaluate side-chains 1160 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 993 time to evaluate : 8.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 0 residue 46 LYS Chi-restraints excluded: chain 0 residue 47 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 ARG Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 179 LYS Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 137 ASN Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 23 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 SER Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 32 ASN Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 86 ASP Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 316 optimal weight: 2.9990 chunk 846 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 551 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 940 optimal weight: 2.9990 chunk 780 optimal weight: 0.0070 chunk 435 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 311 optimal weight: 5.9990 chunk 493 optimal weight: 3.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 120 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN G 45 GLN O 9 GLN O 55 ASN Q 43 ASN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN ** b 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN d 91 ASN d 118 GLN f 58 HIS h 23 GLN h 42 GLN h 86 GLN j 99 GLN o 40 GLN q 31 GLN r 31 GLN r 54 GLN s 65 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 150209 Z= 0.217 Angle : 0.619 15.577 224785 Z= 0.337 Chirality : 0.037 0.351 28732 Planarity : 0.006 0.130 12006 Dihedral : 22.920 179.987 75167 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.88 % Favored : 96.97 % Rotamer: Outliers : 4.44 % Allowed : 23.77 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.76 (0.11), residues: 5414 helix: 1.93 (0.12), residues: 1861 sheet: 0.58 (0.16), residues: 1061 loop : -0.63 (0.11), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 201 HIS 0.008 0.001 HIS f 58 PHE 0.017 0.001 PHE F 175 TYR 0.013 0.001 TYR C 83 ARG 0.014 0.000 ARG b 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1038 time to evaluate : 5.826 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: 0 47 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: 1 1 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7575 (mtp) REVERT: C 5 LYS cc_start: 0.7766 (tptp) cc_final: 0.7424 (tptp) REVERT: C 200 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8226 (t0) REVERT: F 20 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7956 (mm) REVERT: F 57 MET cc_start: 0.7160 (mtp) cc_final: 0.6786 (mtt) REVERT: I 61 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: I 79 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: J 53 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8026 (mmtm) REVERT: J 86 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9043 (mm) REVERT: Q 37 ASP cc_start: 0.8274 (p0) cc_final: 0.7940 (p0) REVERT: R 2 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: S 1 MET cc_start: 0.3289 (OUTLIER) cc_final: 0.2839 (ptt) REVERT: S 8 GLN cc_start: 0.8394 (mm110) cc_final: 0.8180 (mm-40) REVERT: T 42 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8306 (tttp) REVERT: W 72 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8499 (mtt-85) REVERT: b 34 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7178 (t80) REVERT: b 80 ASN cc_start: 0.4895 (t0) cc_final: 0.4567 (t0) REVERT: b 169 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7834 (p0) REVERT: b 191 THR cc_start: 0.7001 (OUTLIER) cc_final: 0.6686 (t) REVERT: c 72 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8188 (mtt-85) REVERT: e 61 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8689 (mttp) REVERT: f 31 GLU cc_start: 0.8904 (pp20) cc_final: 0.8661 (pp20) REVERT: f 58 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.8012 (m-70) REVERT: g 138 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7649 (tpt-90) REVERT: g 144 MET cc_start: 0.7495 (mmt) cc_final: 0.7110 (mmt) REVERT: i 57 GLU cc_start: 0.8049 (mp0) cc_final: 0.7794 (mp0) REVERT: i 128 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7193 (mtm-85) REVERT: l 88 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7659 (tptm) REVERT: s 32 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8519 (ttmm) REVERT: t 18 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8435 (ttm170) REVERT: t 34 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7767 (mtm-85) REVERT: t 35 THR cc_start: 0.9020 (m) cc_final: 0.8801 (m) REVERT: u 63 GLU cc_start: 0.0156 (OUTLIER) cc_final: -0.0912 (mp0) outliers start: 199 outliers final: 111 residues processed: 1152 average time/residue: 2.1670 time to fit residues: 3496.9767 Evaluate side-chains 1138 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1002 time to evaluate : 5.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 46 LYS Chi-restraints excluded: chain 0 residue 47 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 60 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 179 LYS Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 207 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 138 ARG Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 SER Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain t residue 36 LEU Chi-restraints excluded: chain t residue 37 SER Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 906 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 535 optimal weight: 4.9990 chunk 686 optimal weight: 30.0000 chunk 532 optimal weight: 10.0000 chunk 791 optimal weight: 10.0000 chunk 525 optimal weight: 0.7980 chunk 936 optimal weight: 5.9990 chunk 586 optimal weight: 10.0000 chunk 571 optimal weight: 8.9990 chunk 432 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 120 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN O 9 GLN Q 43 ASN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 88 GLN d 118 GLN f 52 ASN f 58 HIS h 23 GLN h 42 GLN h 86 GLN j 99 GLN o 40 GLN q 31 GLN r 31 GLN r 54 GLN s 65 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 150209 Z= 0.357 Angle : 0.681 15.941 224785 Z= 0.364 Chirality : 0.041 0.352 28732 Planarity : 0.006 0.138 12006 Dihedral : 22.917 179.671 75164 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.32 % Favored : 96.53 % Rotamer: Outliers : 4.35 % Allowed : 24.28 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.65 (0.11), residues: 5414 helix: 1.81 (0.12), residues: 1872 sheet: 0.55 (0.16), residues: 1040 loop : -0.68 (0.11), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 172 HIS 0.008 0.001 HIS C 25 PHE 0.022 0.002 PHE F 175 TYR 0.018 0.002 TYR P 32 ARG 0.016 0.001 ARG J 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1020 time to evaluate : 5.794 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: 0 47 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: 1 1 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7632 (mtp) REVERT: C 200 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8224 (t0) REVERT: F 20 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7919 (mm) REVERT: F 57 MET cc_start: 0.7243 (mtp) cc_final: 0.6910 (mtp) REVERT: G 69 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8223 (tpt90) REVERT: I 61 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: I 79 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: J 53 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8042 (mmtm) REVERT: J 86 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9053 (mm) REVERT: J 97 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6264 (mtp180) REVERT: N 10 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7791 (ttm110) REVERT: Q 37 ASP cc_start: 0.8279 (p0) cc_final: 0.7968 (p0) REVERT: R 2 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: S 1 MET cc_start: 0.3207 (OUTLIER) cc_final: 0.2781 (ptt) REVERT: T 42 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8390 (tttp) REVERT: W 72 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8503 (mtt-85) REVERT: X 47 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8607 (ttt90) REVERT: Z 38 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7786 (ttt180) REVERT: b 33 ILE cc_start: 0.8396 (mt) cc_final: 0.7973 (mp) REVERT: b 80 ASN cc_start: 0.5092 (t0) cc_final: 0.4684 (t0) REVERT: b 169 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7845 (p0) REVERT: b 191 THR cc_start: 0.7082 (OUTLIER) cc_final: 0.6799 (t) REVERT: c 72 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8286 (mtt-85) REVERT: e 61 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8711 (mttp) REVERT: f 58 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7956 (m-70) REVERT: g 114 LYS cc_start: 0.7787 (mttp) cc_final: 0.7530 (mttp) REVERT: g 144 MET cc_start: 0.7545 (mmt) cc_final: 0.7162 (mmt) REVERT: i 57 GLU cc_start: 0.8044 (mp0) cc_final: 0.7779 (mp0) REVERT: i 128 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7166 (mtm-85) REVERT: l 88 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7659 (tptm) REVERT: s 32 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8492 (tttm) REVERT: t 18 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8480 (ttm170) REVERT: t 34 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7773 (mtm-85) outliers start: 195 outliers final: 121 residues processed: 1130 average time/residue: 2.2452 time to fit residues: 3541.3313 Evaluate side-chains 1141 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 993 time to evaluate : 5.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 0 residue 46 LYS Chi-restraints excluded: chain 0 residue 47 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 42 LYS Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 ARG Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 179 LYS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 207 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 23 THR Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 32 ASN Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 86 ASP Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain q residue 38 SER Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain t residue 36 LEU Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 579 optimal weight: 2.9990 chunk 374 optimal weight: 7.9990 chunk 559 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 595 optimal weight: 10.0000 chunk 638 optimal weight: 8.9990 chunk 463 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 736 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 120 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN O 9 GLN Q 43 ASN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN ** b 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 88 GLN ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN h 23 GLN h 42 GLN h 86 GLN o 40 GLN q 31 GLN r 31 GLN r 54 GLN s 65 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 150209 Z= 0.458 Angle : 0.742 16.244 224785 Z= 0.392 Chirality : 0.045 0.373 28732 Planarity : 0.007 0.142 12006 Dihedral : 22.956 179.754 75164 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.49 % Favored : 96.40 % Rotamer: Outliers : 4.48 % Allowed : 24.28 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.50 (0.11), residues: 5414 helix: 1.68 (0.12), residues: 1866 sheet: 0.47 (0.16), residues: 1041 loop : -0.76 (0.11), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 172 HIS 0.018 0.001 HIS f 58 PHE 0.025 0.002 PHE D 121 TYR 0.020 0.002 TYR P 32 ARG 0.017 0.001 ARG b 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1005 time to evaluate : 5.858 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: 0 47 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: 1 1 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7672 (mtp) REVERT: C 163 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: C 175 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7100 (ttp80) REVERT: C 200 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8216 (t0) REVERT: F 20 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7832 (mm) REVERT: F 57 MET cc_start: 0.7290 (mtp) cc_final: 0.6967 (mtp) REVERT: G 23 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7818 (tm-30) REVERT: G 69 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7949 (tpt90) REVERT: I 61 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: I 79 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: J 53 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8158 (mmpt) REVERT: J 86 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9045 (mm) REVERT: J 97 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6241 (mtp180) REVERT: M 49 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: Q 37 ASP cc_start: 0.8285 (p0) cc_final: 0.7969 (p0) REVERT: R 2 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: S 1 MET cc_start: 0.3268 (OUTLIER) cc_final: 0.2866 (ptt) REVERT: W 72 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8513 (mtt-85) REVERT: X 47 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8632 (ttt90) REVERT: Z 38 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7814 (ttt180) REVERT: b 9 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7781 (mmt90) REVERT: b 33 ILE cc_start: 0.8389 (mt) cc_final: 0.7955 (mp) REVERT: b 80 ASN cc_start: 0.5035 (t0) cc_final: 0.4729 (t0) REVERT: b 169 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7836 (p0) REVERT: b 191 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6888 (t) REVERT: c 72 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8349 (mtt-85) REVERT: e 61 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8710 (mttp) REVERT: f 46 GLN cc_start: 0.8254 (tp40) cc_final: 0.8025 (tm-30) REVERT: g 114 LYS cc_start: 0.7773 (mttp) cc_final: 0.7451 (mttp) REVERT: g 144 MET cc_start: 0.7565 (mmt) cc_final: 0.7169 (mmt) REVERT: i 57 GLU cc_start: 0.8045 (mp0) cc_final: 0.7803 (mp0) REVERT: i 128 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7233 (mtm-85) REVERT: l 88 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7665 (tptm) REVERT: p 32 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8231 (mtp180) REVERT: s 32 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8508 (tttm) REVERT: t 18 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8511 (ttm170) REVERT: t 34 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7802 (mtm-85) outliers start: 201 outliers final: 126 residues processed: 1121 average time/residue: 2.2878 time to fit residues: 3585.0733 Evaluate side-chains 1147 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 993 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 0 residue 46 LYS Chi-restraints excluded: chain 0 residue 47 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 ARG Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain b residue 9 ARG Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 117 LYS Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 179 LYS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 207 ASP Chi-restraints excluded: chain b residue 227 LYS Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 137 ASN Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 23 THR Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain i residue 95 VAL Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 32 ASN Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 86 ASP Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 27 GLU Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain t residue 36 LEU Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 852 optimal weight: 0.6980 chunk 897 optimal weight: 0.9980 chunk 818 optimal weight: 10.0000 chunk 873 optimal weight: 6.9990 chunk 525 optimal weight: 0.8980 chunk 380 optimal weight: 5.9990 chunk 685 optimal weight: 50.0000 chunk 267 optimal weight: 5.9990 chunk 788 optimal weight: 6.9990 chunk 825 optimal weight: 0.9990 chunk 869 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN G 45 GLN O 9 GLN Q 43 ASN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 88 GLN ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 91 ASN d 118 GLN f 58 HIS h 23 GLN h 42 GLN h 86 GLN j 99 GLN o 40 GLN q 31 GLN r 31 GLN r 54 GLN s 56 ASN s 65 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 150209 Z= 0.180 Angle : 0.610 16.741 224785 Z= 0.332 Chirality : 0.036 0.351 28732 Planarity : 0.006 0.128 12006 Dihedral : 22.874 179.943 75160 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.90 % Favored : 96.99 % Rotamer: Outliers : 3.57 % Allowed : 25.13 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.80 (0.11), residues: 5414 helix: 2.01 (0.12), residues: 1866 sheet: 0.59 (0.16), residues: 1048 loop : -0.62 (0.11), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 172 HIS 0.008 0.001 HIS f 58 PHE 0.018 0.001 PHE F 175 TYR 0.014 0.001 TYR C 83 ARG 0.015 0.000 ARG J 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1029 time to evaluate : 5.923 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: 0 47 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: 1 1 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7596 (mtp) REVERT: C 175 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7217 (ttp80) REVERT: C 200 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8242 (t0) REVERT: F 20 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7912 (mm) REVERT: F 57 MET cc_start: 0.7096 (mtp) cc_final: 0.6791 (mtt) REVERT: G 69 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8289 (tpt90) REVERT: I 79 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: J 53 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8062 (mmtm) REVERT: J 86 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.9030 (mm) REVERT: M 30 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: N 10 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7772 (ttm110) REVERT: Q 37 ASP cc_start: 0.8259 (p0) cc_final: 0.7935 (p0) REVERT: R 2 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: S 1 MET cc_start: 0.3142 (OUTLIER) cc_final: 0.2696 (ptt) REVERT: S 8 GLN cc_start: 0.8398 (mm110) cc_final: 0.8179 (mm-40) REVERT: W 72 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8495 (mtt-85) REVERT: X 47 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8604 (ttt90) REVERT: b 33 ILE cc_start: 0.8407 (mt) cc_final: 0.7983 (mp) REVERT: b 80 ASN cc_start: 0.4989 (t0) cc_final: 0.4676 (t0) REVERT: b 169 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7882 (p0) REVERT: c 72 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8153 (mtt-85) REVERT: g 114 LYS cc_start: 0.7668 (mttp) cc_final: 0.7349 (mttp) REVERT: g 144 MET cc_start: 0.7522 (mmt) cc_final: 0.7144 (mmt) REVERT: i 57 GLU cc_start: 0.8016 (mp0) cc_final: 0.7782 (mp0) REVERT: i 128 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7142 (mtm-85) REVERT: l 88 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7639 (tptm) REVERT: t 18 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8425 (ttm170) REVERT: t 34 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7748 (mtm-85) REVERT: t 35 THR cc_start: 0.8969 (m) cc_final: 0.8758 (m) outliers start: 160 outliers final: 104 residues processed: 1118 average time/residue: 2.2185 time to fit residues: 3479.9864 Evaluate side-chains 1142 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1018 time to evaluate : 5.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 46 LYS Chi-restraints excluded: chain 0 residue 47 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 30 GLU Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 59 GLN Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 179 LYS Chi-restraints excluded: chain b residue 207 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 23 THR Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 13 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain t residue 36 LEU Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 573 optimal weight: 3.9990 chunk 923 optimal weight: 8.9990 chunk 563 optimal weight: 10.0000 chunk 437 optimal weight: 4.9990 chunk 641 optimal weight: 10.0000 chunk 968 optimal weight: 10.0000 chunk 891 optimal weight: 10.0000 chunk 771 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 595 optimal weight: 10.0000 chunk 472 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 120 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN Q 43 ASN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN b 60 ASN ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 88 GLN ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN f 52 ASN f 58 HIS h 23 GLN h 86 GLN j 99 GLN o 40 GLN q 31 GLN r 31 GLN r 54 GLN s 65 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 150209 Z= 0.402 Angle : 0.706 16.875 224785 Z= 0.375 Chirality : 0.043 0.351 28732 Planarity : 0.006 0.140 12006 Dihedral : 22.887 179.629 75155 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.42 % Favored : 96.47 % Rotamer: Outliers : 3.46 % Allowed : 25.62 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 5414 helix: 1.80 (0.12), residues: 1878 sheet: 0.55 (0.16), residues: 1054 loop : -0.69 (0.11), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 172 HIS 0.008 0.001 HIS f 58 PHE 0.023 0.002 PHE D 121 TYR 0.020 0.002 TYR P 32 ARG 0.012 0.001 ARG C 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10828 Ramachandran restraints generated. 5414 Oldfield, 0 Emsley, 5414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1011 time to evaluate : 5.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 47 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: 1 1 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7651 (mtp) REVERT: C 200 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8210 (t0) REVERT: F 20 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7905 (mm) REVERT: F 38 MET cc_start: 0.7161 (mtt) cc_final: 0.6603 (ptp) REVERT: F 57 MET cc_start: 0.7171 (mtp) cc_final: 0.6751 (mtt) REVERT: G 69 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8128 (tpt90) REVERT: I 79 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: J 53 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8060 (mmtm) REVERT: J 97 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6221 (mtp180) REVERT: Q 37 ASP cc_start: 0.8274 (p0) cc_final: 0.7953 (p0) REVERT: R 2 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: S 1 MET cc_start: 0.3247 (OUTLIER) cc_final: 0.2836 (ptt) REVERT: S 8 GLN cc_start: 0.8411 (mm110) cc_final: 0.8198 (mm-40) REVERT: W 72 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8496 (mtt-85) REVERT: X 47 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8625 (ttt90) REVERT: Z 38 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7798 (ttt180) REVERT: b 33 ILE cc_start: 0.8418 (mt) cc_final: 0.7993 (mp) REVERT: b 80 ASN cc_start: 0.4946 (t0) cc_final: 0.4645 (t0) REVERT: b 169 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7830 (p0) REVERT: b 191 THR cc_start: 0.7156 (OUTLIER) cc_final: 0.6891 (t) REVERT: c 72 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8313 (mtt-85) REVERT: g 114 LYS cc_start: 0.7719 (mttp) cc_final: 0.7387 (mttp) REVERT: g 144 MET cc_start: 0.7535 (mmt) cc_final: 0.7160 (mmt) REVERT: i 57 GLU cc_start: 0.8054 (mp0) cc_final: 0.7803 (mp0) REVERT: i 128 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7200 (mtm-85) REVERT: l 88 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7640 (tptm) REVERT: p 32 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8232 (mtp180) REVERT: t 18 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8480 (ttm170) REVERT: t 34 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7780 (mtm-85) outliers start: 155 outliers final: 112 residues processed: 1101 average time/residue: 2.2530 time to fit residues: 3467.6128 Evaluate side-chains 1134 residues out of total 4485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1001 time to evaluate : 5.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 46 LYS Chi-restraints excluded: chain 0 residue 47 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 2 GLU Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 24 LYS Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 9 LYS Chi-restraints excluded: chain X residue 47 ARG Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 ARG Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 179 LYS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 207 ASP Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 215 MET Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 175 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 102 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 SER Chi-restraints excluded: chain i residue 23 THR Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain l residue 4 THR Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 38 SER Chi-restraints excluded: chain r residue 22 ASP Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain t residue 36 LEU Chi-restraints excluded: chain t residue 86 LEU Chi-restraints excluded: chain u residue 63 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 612 optimal weight: 7.9990 chunk 821 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 711 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 214 optimal weight: 5.9990 chunk 772 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 793 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 120 ASN C 163 GLN O 9 GLN Q 43 ASN T 9 GLN ** T 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN Y 48 ASN ** b 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 88 GLN c 139 GLN d 118 GLN f 58 HIS h 23 GLN h 86 GLN j 35 GLN j 99 GLN o 40 GLN q 31 GLN r 31 GLN r 54 GLN s 65 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.084426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.054280 restraints weight = 245965.605| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 0.96 r_work: 0.2559 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 150209 Z= 0.415 Angle : 0.726 17.294 224785 Z= 0.385 Chirality : 0.043 0.353 28732 Planarity : 0.007 0.141 12006 Dihedral : 22.943 179.638 75154 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.53 % Favored : 96.36 % Rotamer: Outliers : 3.43 % Allowed : 25.64 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.52 (0.11), residues: 5414 helix: 1.70 (0.12), residues: 1876 sheet: 0.45 (0.16), residues: 1043 loop : -0.75 (0.11), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP d 172 HIS 0.009 0.001 HIS C 25 PHE 0.024 0.002 PHE D 121 TYR 0.019 0.002 TYR P 32 ARG 0.019 0.001 ARG J 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51030.46 seconds wall clock time: 880 minutes 36.49 seconds (52836.49 seconds total)