Starting phenix.real_space_refine on Mon Feb 19 12:55:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/02_2024/6p4g_20248.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/02_2024/6p4g_20248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/02_2024/6p4g_20248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/02_2024/6p4g_20248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/02_2024/6p4g_20248.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/02_2024/6p4g_20248.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1899 5.49 5 S 184 5.16 5 C 42639 2.51 5 N 14588 2.21 5 O 20064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 63": "NH1" <-> "NH2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 198": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "I PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 12": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ARG 141": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 138": "NH1" <-> "NH2" Residue "K PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ASP 110": "OD1" <-> "OD2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ASP 138": "OD1" <-> "OD2" Residue "P ARG 141": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 130": "NH1" <-> "NH2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "T PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 121": "NH1" <-> "NH2" Residue "U ARG 16": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "U ARG 102": "NH1" <-> "NH2" Residue "U ARG 121": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 87": "NH1" <-> "NH2" Residue "W TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 38": "OE1" <-> "OE2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 54": "OD1" <-> "OD2" Residue "X PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 8": "NH1" <-> "NH2" Residue "Y ARG 17": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 67": "NH1" <-> "NH2" Residue "Y PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 107": "NH1" <-> "NH2" Residue "Z ARG 20": "NH1" <-> "NH2" Residue "Z PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z ARG 110": "NH1" <-> "NH2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "c ARG 72": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ASP 37": "OD1" <-> "OD2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 66": "NH1" <-> "NH2" Residue "d ARG 67": "NH1" <-> "NH2" Residue "e PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 81": "NH1" <-> "NH2" Residue "f ARG 101": "NH1" <-> "NH2" Residue "f ARG 104": "NH1" <-> "NH2" Residue "g TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 47": "NH1" <-> "NH2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h ARG 100": "NH1" <-> "NH2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 9": "NH1" <-> "NH2" Residue "n ARG 15": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 79374 Number of models: 1 Model: "" Number of chains: 36 Chain: "2" Number of atoms: 36229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36229 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 145, 'rna2p_pyr': 109, 'rna3p_pur': 753, 'rna3p_pyr': 690} Link IDs: {'rna2p': 253, 'rna3p': 1443} Chain breaks: 11 Chain: "B" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1706 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1712 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2073 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1462 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1175 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 990 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 124} Chain: "T" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1168 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 3, 'TRANS': 137} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 557 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "b" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 778 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "1" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 4323 Classifications: {'RNA': 203} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 12, 'rna3p_pur': 87, 'rna3p_pyr': 86} Link IDs: {'rna2p': 30, 'rna3p': 172} Time building chain proxies: 30.98, per 1000 atoms: 0.39 Number of scatterers: 79374 At special positions: 0 Unit cell: (234.27, 261.396, 209.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 1899 15.00 O 20064 8.00 N 14588 7.00 C 42639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 26 " distance=1.89 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 74 " distance=2.37 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 77 " distance=1.94 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 74 " distance=1.86 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=2.33 Simple disulfide: pdb=" SG CYS b 74 " - pdb=" SG CYS b 77 " distance=1.90 Simple disulfide: pdb=" SG CYS e 21 " - pdb=" SG CYS e 24 " distance=2.04 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 39 " distance=2.05 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 42 " distance=1.98 Simple disulfide: pdb=" SG CYS e 39 " - pdb=" SG CYS e 42 " distance=2.09 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: 29.52 Conformation dependent library (CDL) restraints added in 5.4 seconds 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9018 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 58 sheets defined 34.9% alpha, 17.2% beta 512 base pairs and 1013 stacking pairs defined. Time for finding SS restraints: 24.90 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.513A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.739A pdb=" N GLU B 35 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.689A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 removed outlier: 4.604A pdb=" N ALA B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.794A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.514A pdb=" N GLU B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.683A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 192 through 201 removed outlier: 3.519A pdb=" N GLU C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.576A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 77 through 84 removed outlier: 3.642A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.517A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 98 " --> pdb=" O ILE D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 162 Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 247 through 250 removed outlier: 3.798A pdb=" N TYR D 250 " --> pdb=" O THR D 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 250' Processing helix chain 'D' and resid 252 through 257 removed outlier: 4.596A pdb=" N LYS D 257 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 269 through 277 removed outlier: 3.612A pdb=" N MET D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 54 through 60 removed outlier: 3.561A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.689A pdb=" N ARG E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.545A pdb=" N LEU E 96 " --> pdb=" O THR E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 114 through 130 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'F' and resid 10 through 14 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.948A pdb=" N VAL F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 247 through 263 removed outlier: 3.762A pdb=" N GLY F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 61 through 66 Processing helix chain 'G' and resid 67 through 77 removed outlier: 3.816A pdb=" N MET G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 3.705A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.931A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 163 removed outlier: 3.515A pdb=" N ALA G 161 " --> pdb=" O GLY G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 187 through 203 removed outlier: 3.580A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 153 through 157 removed outlier: 3.834A pdb=" N VAL H 157 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 237 removed outlier: 4.767A pdb=" N LYS H 195 " --> pdb=" O ARG H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 32 Processing helix chain 'I' and resid 36 through 40 Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 68 through 75 removed outlier: 3.700A pdb=" N LYS I 74 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.175A pdb=" N GLU I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 132 removed outlier: 3.708A pdb=" N LEU I 130 " --> pdb=" O HIS I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 167 Processing helix chain 'I' and resid 169 through 182 removed outlier: 3.544A pdb=" N GLY I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 93 removed outlier: 3.680A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 135 through 139 removed outlier: 3.586A pdb=" N ASN J 138 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS J 139 " --> pdb=" O ILE J 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 135 through 139' Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.833A pdb=" N GLN J 146 " --> pdb=" O SER J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 168 removed outlier: 3.603A pdb=" N GLN J 167 " --> pdb=" O GLU J 163 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN J 168 " --> pdb=" O GLU J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 183 Processing helix chain 'J' and resid 191 through 207 removed outlier: 3.642A pdb=" N LEU J 195 " --> pdb=" O GLU J 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 36 removed outlier: 3.660A pdb=" N LYS K 30 " --> pdb=" O ASP K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 63 removed outlier: 3.897A pdb=" N VAL K 46 " --> pdb=" O GLU K 42 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 101 through 107 removed outlier: 3.971A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 171 through 186 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.509A pdb=" N LEU L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.626A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 53 removed outlier: 3.753A pdb=" N ILE M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 27 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 81 through 89 removed outlier: 3.525A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 128 removed outlier: 4.164A pdb=" N VAL N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 44 Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 70 through 79 removed outlier: 3.833A pdb=" N LYS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 102 Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 70 through 88 removed outlier: 3.747A pdb=" N GLU P 87 " --> pdb=" O GLN P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.515A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 34 Processing helix chain 'Q' and resid 38 through 47 Processing helix chain 'Q' and resid 52 through 54 No H-bonds generated for 'chain 'Q' and resid 52 through 54' Processing helix chain 'Q' and resid 55 through 65 removed outlier: 3.711A pdb=" N LYS Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 112 removed outlier: 3.704A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 120 removed outlier: 3.587A pdb=" N SER Q 120 " --> pdb=" O GLY Q 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 42 Processing helix chain 'R' and resid 44 through 48 removed outlier: 3.700A pdb=" N LEU R 47 " --> pdb=" O PRO R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 59 removed outlier: 3.503A pdb=" N LEU R 58 " --> pdb=" O PRO R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.609A pdb=" N ILE R 88 " --> pdb=" O ILE R 84 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.652A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.861A pdb=" N ALA S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 38 removed outlier: 3.525A pdb=" N ARG S 33 " --> pdb=" O HIS S 29 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 63 Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'S' and resid 99 through 107 Processing helix chain 'T' and resid 25 through 30 Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.627A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.521A pdb=" N THR T 69 " --> pdb=" O GLU T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 84 Processing helix chain 'T' and resid 99 through 117 removed outlier: 3.665A pdb=" N LEU T 114 " --> pdb=" O ASP T 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 127 Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 10 through 26 removed outlier: 4.318A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 35 removed outlier: 3.858A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.972A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.563A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU U 108 " --> pdb=" O LEU U 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 142 Processing helix chain 'V' and resid 28 through 46 removed outlier: 3.522A pdb=" N LEU V 32 " --> pdb=" O ASN V 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS V 46 " --> pdb=" O GLY V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 102 removed outlier: 3.646A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.568A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 removed outlier: 3.514A pdb=" N HIS X 44 " --> pdb=" O VAL X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.667A pdb=" N LEU X 94 " --> pdb=" O GLN X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 119 removed outlier: 3.606A pdb=" N ARG X 118 " --> pdb=" O GLU X 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 21 Processing helix chain 'Y' and resid 24 through 31 removed outlier: 3.697A pdb=" N ALA Y 30 " --> pdb=" O GLN Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 39 removed outlier: 4.156A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.615A pdb=" N MET Z 47 " --> pdb=" O LYS Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing helix chain 'Z' and resid 78 through 83 Processing helix chain 'Z' and resid 87 through 93 Processing helix chain 'Z' and resid 103 through 115 Processing helix chain 'Z' and resid 118 through 124 removed outlier: 4.049A pdb=" N ALA Z 121 " --> pdb=" O ARG Z 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.598A pdb=" N TYR a 55 " --> pdb=" O ASP a 51 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 77 removed outlier: 3.615A pdb=" N GLU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 94 removed outlier: 3.515A pdb=" N LEU a 92 " --> pdb=" O LEU a 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 56 removed outlier: 3.714A pdb=" N SER b 54 " --> pdb=" O VAL b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.512A pdb=" N ARG c 17 " --> pdb=" O GLU c 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 32 through 36 Processing helix chain 'e' and resid 41 through 51 removed outlier: 5.737A pdb=" N LYS e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP e 49 " --> pdb=" O GLN e 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 78 through 82 removed outlier: 3.575A pdb=" N ARG f 81 " --> pdb=" O SER f 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL f 82 " --> pdb=" O LEU f 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 78 through 82' Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 103 through 115 Processing helix chain 'g' and resid 101 through 106 Processing helix chain 'n' and resid 2 through 16 Processing helix chain 'n' and resid 16 through 21 removed outlier: 4.043A pdb=" N MET n 20 " --> pdb=" O LYS n 16 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.123A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.195A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 120 through 128 removed outlier: 6.617A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 128 removed outlier: 3.827A pdb=" N LYS C 219 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG C 136 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N MET C 217 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 103 through 114 removed outlier: 5.885A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 39 removed outlier: 3.910A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AA9, first strand: chain 'E' and resid 209 through 210 Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 43 removed outlier: 3.563A pdb=" N ALA F 84 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.226A pdb=" N HIS F 112 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.785A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 180 through 182 removed outlier: 5.243A pdb=" N ILE F 195 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS F 211 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN F 197 " --> pdb=" O HIS F 209 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AB6, first strand: chain 'G' and resid 123 through 126 removed outlier: 8.471A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE d 42 " --> pdb=" O VAL d 32 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 12 through 16 removed outlier: 6.817A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 12 through 16 removed outlier: 6.825A pdb=" N ASN H 56 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 72 through 76 Processing sheet with id=AC1, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.514A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG H 170 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 49 through 53 removed outlier: 4.396A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 185 through 188 removed outlier: 3.694A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 36 through 37 removed outlier: 4.363A pdb=" N THR J 36 " --> pdb=" O LEU J 96 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.474A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 62 through 66 removed outlier: 8.045A pdb=" N ILE J 79 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ASP J 105 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL J 81 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU J 103 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.502A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AC9, first strand: chain 'M' and resid 101 through 107 removed outlier: 4.855A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) removed outlier: 18.363A pdb=" N ILE M 72 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 15.156A pdb=" N LEU M 93 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N SER M 74 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP M 91 " --> pdb=" O SER M 74 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 32 through 33 removed outlier: 4.162A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 51 through 52 Processing sheet with id=AD3, first strand: chain 'P' and resid 34 through 36 removed outlier: 3.850A pdb=" N ASP P 39 " --> pdb=" O SER P 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 34 through 36 removed outlier: 3.850A pdb=" N ASP P 39 " --> pdb=" O SER P 36 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 76 through 78 Processing sheet with id=AD6, first strand: chain 'R' and resid 9 through 15 Processing sheet with id=AD7, first strand: chain 'S' and resid 96 through 98 removed outlier: 6.148A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'T' and resid 12 through 15 Processing sheet with id=AD9, first strand: chain 'U' and resid 81 through 83 Processing sheet with id=AE1, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE2, first strand: chain 'V' and resid 50 through 63 removed outlier: 3.642A pdb=" N ASP V 90 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU V 88 " --> pdb=" O PRO V 53 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG V 55 " --> pdb=" O LYS V 86 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LYS V 86 " --> pdb=" O ARG V 55 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE V 84 " --> pdb=" O PRO V 57 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS V 59 " --> pdb=" O MET V 82 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N MET V 82 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU V 61 " --> pdb=" O PHE V 80 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE V 80 " --> pdb=" O LEU V 61 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 32 through 39 removed outlier: 3.549A pdb=" N VAL W 36 " --> pdb=" O LYS W 51 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 71 through 74 Processing sheet with id=AE5, first strand: chain 'X' and resid 80 through 81 removed outlier: 3.587A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 128 through 129 removed outlier: 6.630A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE Y 120 " --> pdb=" O THR Y 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 6 through 15 removed outlier: 5.459A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'a' and resid 98 through 102 removed outlier: 6.905A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF1, first strand: chain 'b' and resid 38 through 43 Processing sheet with id=AF2, first strand: chain 'c' and resid 44 through 47 removed outlier: 4.466A pdb=" N PHE c 32 " --> pdb=" O LYS c 82 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 64 through 65 Processing sheet with id=AF4, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.542A pdb=" N MET e 38 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 133 through 134 removed outlier: 3.612A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 5 through 6 removed outlier: 3.715A pdb=" N VAL h 307 " --> pdb=" O LEU h 11 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AF8, first strand: chain 'h' and resid 21 through 22 removed outlier: 3.503A pdb=" N LEU h 32 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.603A pdb=" N THR h 96 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 120 through 123 removed outlier: 3.804A pdb=" N ILE h 120 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE h 129 " --> pdb=" O VAL h 142 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 153 through 156 removed outlier: 3.975A pdb=" N CYS h 153 " --> pdb=" O CYS h 168 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 195 through 200 removed outlier: 5.495A pdb=" N GLY h 211 " --> pdb=" O GLN h 215 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN h 215 " --> pdb=" O GLY h 211 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU h 218 " --> pdb=" O TYR h 228 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR h 228 " --> pdb=" O LEU h 218 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP h 220 " --> pdb=" O HIS h 226 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS h 226 " --> pdb=" O ASP h 220 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 236 through 241 removed outlier: 3.730A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) 1472 hydrogen bonds defined for protein. 4140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1276 hydrogen bonds 2082 hydrogen bond angles 0 basepair planarities 512 basepair parallelities 1013 stacking parallelities Total time for adding SS restraints: 65.34 Time building geometry restraints manager: 32.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11868 1.33 - 1.46: 33012 1.46 - 1.59: 35955 1.59 - 1.71: 3708 1.71 - 1.84: 280 Bond restraints: 84823 Sorted by residual: bond pdb=" N ILE H 121 " pdb=" CA ILE H 121 " ideal model delta sigma weight residual 1.454 1.494 -0.039 7.70e-03 1.69e+04 2.57e+01 bond pdb=" N VAL L 40 " pdb=" CA VAL L 40 " ideal model delta sigma weight residual 1.460 1.497 -0.038 7.50e-03 1.78e+04 2.54e+01 bond pdb=" N VAL U 30 " pdb=" CA VAL U 30 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.38e+01 bond pdb=" N GLU V 107 " pdb=" CA GLU V 107 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 2.03e+01 bond pdb=" N ILE K 144 " pdb=" CA ILE K 144 " ideal model delta sigma weight residual 1.456 1.495 -0.038 8.70e-03 1.32e+04 1.96e+01 ... (remaining 84818 not shown) Histogram of bond angle deviations from ideal: 97.31 - 104.81: 8792 104.81 - 112.31: 43865 112.31 - 119.81: 38086 119.81 - 127.31: 28705 127.31 - 134.81: 4171 Bond angle restraints: 123619 Sorted by residual: angle pdb=" C ASP P 138 " pdb=" CA ASP P 138 " pdb=" CB ASP P 138 " ideal model delta sigma weight residual 109.71 129.02 -19.31 1.83e+00 2.99e-01 1.11e+02 angle pdb=" O3' U 2 688 " pdb=" C3' U 2 688 " pdb=" C2' U 2 688 " ideal model delta sigma weight residual 109.50 123.97 -14.47 1.50e+00 4.44e-01 9.30e+01 angle pdb=" O3' A 21489 " pdb=" C3' A 21489 " pdb=" C2' A 21489 " ideal model delta sigma weight residual 109.50 123.28 -13.78 1.50e+00 4.44e-01 8.45e+01 angle pdb=" C4' A 21476 " pdb=" C3' A 21476 " pdb=" O3' A 21476 " ideal model delta sigma weight residual 109.40 122.79 -13.39 1.50e+00 4.44e-01 7.97e+01 angle pdb=" C4' A 21664 " pdb=" C3' A 21664 " pdb=" O3' A 21664 " ideal model delta sigma weight residual 109.40 122.60 -13.20 1.50e+00 4.44e-01 7.75e+01 ... (remaining 123614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 48612 35.99 - 71.97: 4843 71.97 - 107.96: 599 107.96 - 143.94: 29 143.94 - 179.93: 53 Dihedral angle restraints: 54136 sinusoidal: 40159 harmonic: 13977 Sorted by residual: dihedral pdb=" C ASP P 138 " pdb=" N ASP P 138 " pdb=" CA ASP P 138 " pdb=" CB ASP P 138 " ideal model delta harmonic sigma weight residual -122.60 -160.78 38.18 0 2.50e+00 1.60e-01 2.33e+02 dihedral pdb=" N ASP P 138 " pdb=" C ASP P 138 " pdb=" CA ASP P 138 " pdb=" CB ASP P 138 " ideal model delta harmonic sigma weight residual 122.80 157.55 -34.75 0 2.50e+00 1.60e-01 1.93e+02 dihedral pdb=" C5' A 16541 " pdb=" C4' A 16541 " pdb=" C3' A 16541 " pdb=" O3' A 16541 " ideal model delta sinusoidal sigma weight residual 147.00 62.12 84.88 1 8.00e+00 1.56e-02 1.37e+02 ... (remaining 54133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.313: 15338 0.313 - 0.626: 20 0.626 - 0.938: 4 0.938 - 1.251: 0 1.251 - 1.564: 1 Chirality restraints: 15363 Sorted by residual: chirality pdb=" CA ASP P 138 " pdb=" N ASP P 138 " pdb=" C ASP P 138 " pdb=" CB ASP P 138 " both_signs ideal model delta sigma weight residual False 2.51 0.95 1.56 2.00e-01 2.50e+01 6.12e+01 chirality pdb=" C3' U 2 688 " pdb=" C4' U 2 688 " pdb=" O3' U 2 688 " pdb=" C2' U 2 688 " both_signs ideal model delta sigma weight residual False -2.74 -1.98 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C3' U 21377 " pdb=" C4' U 21377 " pdb=" O3' U 21377 " pdb=" C2' U 21377 " both_signs ideal model delta sigma weight residual False -2.48 -1.80 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 15360 not shown) Planarity restraints: 8630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 59 " -0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ALA Y 59 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA Y 59 " -0.029 2.00e-02 2.50e+03 pdb=" N LYS Y 60 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Q 118 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLU Q 118 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU Q 118 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE Q 119 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO P 136 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.58e+00 pdb=" C PRO P 136 " -0.053 2.00e-02 2.50e+03 pdb=" O PRO P 136 " 0.021 2.00e-02 2.50e+03 pdb=" N SER P 137 " 0.018 2.00e-02 2.50e+03 ... (remaining 8627 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 10409 2.77 - 3.30: 70725 3.30 - 3.83: 151350 3.83 - 4.37: 194231 4.37 - 4.90: 268763 Nonbonded interactions: 695478 Sorted by model distance: nonbonded pdb=" OH TYR W 53 " pdb=" O LEU W 72 " model vdw 2.232 2.440 nonbonded pdb=" O2' A 16541 " pdb=" OP1 U 16542 " model vdw 2.235 2.440 nonbonded pdb=" O4' C 2 369 " pdb=" O2 C 2 369 " model vdw 2.247 3.040 nonbonded pdb=" O4' C 2 853 " pdb=" O2 C 2 853 " model vdw 2.254 3.040 nonbonded pdb=" O4' C 21117 " pdb=" O2 C 21117 " model vdw 2.254 3.040 ... (remaining 695473 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 9.160 Check model and map are aligned: 0.880 Set scattering table: 0.530 Process input model: 212.140 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 229.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.010 0.054 84823 Z= 0.646 Angle : 1.453 19.313 123619 Z= 1.029 Chirality : 0.101 1.564 15363 Planarity : 0.004 0.045 8630 Dihedral : 23.131 179.925 45088 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.90 % Favored : 90.23 % Rotamer: Outliers : 3.36 % Allowed : 7.63 % Favored : 89.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.22 % 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: -4.06 (0.10), residues: 4788 helix: -2.98 (0.09), residues: 1486 sheet: -2.76 (0.15), residues: 811 loop : -2.45 (0.11), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP h 17 HIS 0.011 0.002 HIS G 79 PHE 0.029 0.003 PHE I 135 TYR 0.028 0.003 TYR M 99 ARG 0.011 0.001 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1423 time to evaluate : 4.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 ASP cc_start: 0.8340 (m-30) cc_final: 0.7481 (p0) REVERT: B 35 GLU cc_start: 0.7458 (tt0) cc_final: 0.7146 (tp30) REVERT: B 44 ASP cc_start: 0.7041 (t70) cc_final: 0.6778 (p0) REVERT: B 52 LYS cc_start: 0.7658 (tttt) cc_final: 0.6557 (mttp) REVERT: B 55 TRP cc_start: 0.7437 (t-100) cc_final: 0.6792 (t-100) REVERT: B 69 GLU cc_start: 0.7695 (tt0) cc_final: 0.7490 (tm-30) REVERT: B 75 SER cc_start: 0.8770 (t) cc_final: 0.8406 (m) REVERT: B 84 GLN cc_start: 0.8147 (mt0) cc_final: 0.7831 (mt0) REVERT: B 111 GLN cc_start: 0.7578 (pm20) cc_final: 0.7321 (pm20) REVERT: B 117 ARG cc_start: 0.6896 (mmt90) cc_final: 0.6307 (mmm160) REVERT: B 135 MET cc_start: 0.6081 (mmm) cc_final: 0.5514 (mmt) REVERT: B 149 ASN cc_start: 0.8619 (t0) cc_final: 0.8106 (t0) REVERT: B 152 SER cc_start: 0.7113 (m) cc_final: 0.6909 (m) REVERT: B 189 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7179 (pt) REVERT: B 198 MET cc_start: 0.7644 (ttt) cc_final: 0.7443 (ttp) REVERT: B 203 PHE cc_start: 0.8155 (m-10) cc_final: 0.7693 (m-80) REVERT: C 27 LYS cc_start: 0.7938 (mttp) cc_final: 0.7366 (mmtt) REVERT: C 42 ARG cc_start: 0.6315 (tpp-160) cc_final: 0.6098 (mmm-85) REVERT: C 57 ILE cc_start: 0.6784 (mt) cc_final: 0.6465 (mm) REVERT: C 77 ASP cc_start: 0.7444 (t70) cc_final: 0.7207 (m-30) REVERT: C 82 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7397 (ttm110) REVERT: C 104 ASP cc_start: 0.8170 (m-30) cc_final: 0.7906 (t0) REVERT: C 112 SER cc_start: 0.8512 (t) cc_final: 0.8140 (p) REVERT: C 115 LYS cc_start: 0.7535 (mtmp) cc_final: 0.7031 (mttp) REVERT: C 171 ILE cc_start: 0.7956 (mt) cc_final: 0.7705 (mt) REVERT: C 177 GLN cc_start: 0.7846 (mt0) cc_final: 0.7514 (mt0) REVERT: C 195 LYS cc_start: 0.6985 (mmpt) cc_final: 0.6215 (pttm) REVERT: C 230 GLU cc_start: 0.7792 (tt0) cc_final: 0.6997 (tp30) REVERT: D 63 VAL cc_start: 0.7995 (t) cc_final: 0.7649 (p) REVERT: D 66 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7157 (tp) REVERT: D 68 ARG cc_start: 0.7992 (tpm170) cc_final: 0.7489 (tpp-160) REVERT: D 72 ASP cc_start: 0.6819 (m-30) cc_final: 0.5915 (m-30) REVERT: D 88 ILE cc_start: 0.8145 (mt) cc_final: 0.7868 (mp) REVERT: D 90 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7589 (mm-30) REVERT: D 105 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6219 (tp30) REVERT: D 121 ARG cc_start: 0.7087 (tpm-80) cc_final: 0.6531 (ttt-90) REVERT: D 145 LYS cc_start: 0.8155 (mttm) cc_final: 0.7229 (ptmt) REVERT: D 146 GLU cc_start: 0.7953 (pm20) cc_final: 0.7710 (pm20) REVERT: D 155 ILE cc_start: 0.8213 (mt) cc_final: 0.7920 (mm) REVERT: D 159 LYS cc_start: 0.8121 (mttt) cc_final: 0.7883 (mttt) REVERT: D 166 ARG cc_start: 0.8553 (ttt90) cc_final: 0.8058 (ttt90) REVERT: D 173 LYS cc_start: 0.7170 (mtmt) cc_final: 0.6738 (mtmt) REVERT: D 180 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7967 (m) REVERT: D 185 THR cc_start: 0.8752 (t) cc_final: 0.8471 (m) REVERT: D 242 ASP cc_start: 0.8304 (t0) cc_final: 0.8093 (t0) REVERT: D 246 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7632 (mttm) REVERT: D 250 TYR cc_start: 0.8280 (t80) cc_final: 0.8039 (t80) REVERT: D 277 HIS cc_start: 0.3377 (OUTLIER) cc_final: 0.2468 (p-80) REVERT: E 28 GLU cc_start: 0.7131 (tp30) cc_final: 0.6831 (mm-30) REVERT: E 49 ILE cc_start: 0.6259 (mt) cc_final: 0.6047 (mm) REVERT: E 51 LEU cc_start: 0.5967 (tp) cc_final: 0.5514 (tp) REVERT: E 74 GLN cc_start: 0.6717 (OUTLIER) cc_final: 0.6308 (pp30) REVERT: E 85 GLU cc_start: 0.5867 (pt0) cc_final: 0.5465 (tp30) REVERT: E 86 LEU cc_start: 0.7729 (mp) cc_final: 0.7201 (mp) REVERT: E 87 TYR cc_start: 0.5178 (m-80) cc_final: 0.4391 (m-80) REVERT: E 104 SER cc_start: 0.7882 (t) cc_final: 0.7537 (p) REVERT: E 116 ARG cc_start: 0.6892 (mmt90) cc_final: 0.6314 (mtp180) REVERT: E 117 ARG cc_start: 0.7613 (mmm160) cc_final: 0.6688 (mtt180) REVERT: E 119 CYS cc_start: 0.8104 (m) cc_final: 0.7641 (m) REVERT: E 128 GLU cc_start: 0.6989 (tt0) cc_final: 0.6599 (tp30) REVERT: E 143 ARG cc_start: 0.4653 (ttp80) cc_final: 0.4093 (mmm-85) REVERT: E 157 MET cc_start: 0.8051 (tpp) cc_final: 0.7752 (tpt) REVERT: E 178 ARG cc_start: 0.6475 (ptt90) cc_final: 0.5720 (ttm110) REVERT: F 32 SER cc_start: 0.7708 (OUTLIER) cc_final: 0.7378 (p) REVERT: F 71 LYS cc_start: 0.6858 (ttpt) cc_final: 0.6240 (mtmt) REVERT: F 87 MET cc_start: 0.7920 (mmt) cc_final: 0.7522 (mmt) REVERT: F 118 GLU cc_start: 0.7328 (tt0) cc_final: 0.6523 (tm-30) REVERT: F 120 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6779 (tppt) REVERT: F 148 ARG cc_start: 0.7289 (ptm160) cc_final: 0.7048 (ptm160) REVERT: F 212 ASP cc_start: 0.7610 (t70) cc_final: 0.7339 (t70) REVERT: G 24 SER cc_start: 0.7972 (t) cc_final: 0.7724 (p) REVERT: G 25 THR cc_start: 0.7986 (m) cc_final: 0.7683 (t) REVERT: G 34 SER cc_start: 0.7863 (t) cc_final: 0.7597 (m) REVERT: G 47 LYS cc_start: 0.8311 (mmtt) cc_final: 0.8023 (mmtt) REVERT: G 55 ARG cc_start: 0.7695 (mtp85) cc_final: 0.7399 (mtm110) REVERT: G 76 MET cc_start: 0.8157 (mmm) cc_final: 0.7060 (tpp) REVERT: G 102 LEU cc_start: 0.7381 (mt) cc_final: 0.7078 (tp) REVERT: G 106 GLU cc_start: 0.6798 (tt0) cc_final: 0.6345 (tt0) REVERT: G 123 GLU cc_start: 0.9103 (tt0) cc_final: 0.8893 (tt0) REVERT: G 136 ARG cc_start: 0.7490 (mmm-85) cc_final: 0.6930 (mtp180) REVERT: G 160 GLU cc_start: 0.8121 (tt0) cc_final: 0.7885 (mt-10) REVERT: G 169 ILE cc_start: 0.6171 (OUTLIER) cc_final: 0.5695 (mm) REVERT: H 2 LYS cc_start: 0.5152 (mtmm) cc_final: 0.4501 (mttt) REVERT: H 17 GLU cc_start: 0.7417 (pt0) cc_final: 0.6827 (tt0) REVERT: H 22 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6604 (ttt-90) REVERT: H 30 LYS cc_start: 0.6376 (mmtm) cc_final: 0.5932 (mmtt) REVERT: H 32 MET cc_start: 0.7027 (ttm) cc_final: 0.6687 (mtp) REVERT: H 63 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6414 (mtt) REVERT: H 84 TYR cc_start: 0.7800 (t80) cc_final: 0.7513 (t80) REVERT: H 120 ASP cc_start: 0.5286 (t70) cc_final: 0.4958 (t0) REVERT: H 149 LYS cc_start: 0.6170 (mtmt) cc_final: 0.5003 (mmmt) REVERT: H 154 ARG cc_start: 0.7267 (mtt-85) cc_final: 0.6891 (mtm-85) REVERT: H 155 GLN cc_start: 0.5557 (mt0) cc_final: 0.5029 (mm-40) REVERT: H 170 ARG cc_start: 0.5516 (ttm-80) cc_final: 0.5148 (mtt-85) REVERT: H 197 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8241 (mt0) REVERT: I 25 GLN cc_start: 0.4000 (mt0) cc_final: 0.3739 (mt0) REVERT: I 27 LEU cc_start: 0.6642 (mt) cc_final: 0.6406 (mt) REVERT: I 58 LYS cc_start: 0.7057 (mttt) cc_final: 0.6532 (mttm) REVERT: I 117 PRO cc_start: 0.6262 (Cg_endo) cc_final: 0.5574 (Cg_exo) REVERT: I 133 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6299 (tm) REVERT: I 179 LYS cc_start: 0.7351 (tptm) cc_final: 0.7032 (tptp) REVERT: J 8 TRP cc_start: 0.8366 (p-90) cc_final: 0.8023 (p-90) REVERT: J 28 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7891 (mt-10) REVERT: J 44 HIS cc_start: 0.8487 (m170) cc_final: 0.8177 (m170) REVERT: J 52 ASN cc_start: 0.8041 (m-40) cc_final: 0.7730 (m-40) REVERT: J 55 TYR cc_start: 0.8442 (m-80) cc_final: 0.8194 (m-80) REVERT: J 67 TRP cc_start: 0.7339 (t60) cc_final: 0.6876 (t60) REVERT: J 87 ASN cc_start: 0.6626 (t0) cc_final: 0.6293 (t0) REVERT: J 92 ARG cc_start: 0.7123 (tmm-80) cc_final: 0.6758 (mtm110) REVERT: J 119 LEU cc_start: 0.8461 (mt) cc_final: 0.8120 (mt) REVERT: J 128 LYS cc_start: 0.5685 (mtpt) cc_final: 0.5316 (tptt) REVERT: J 150 ASP cc_start: 0.8004 (m-30) cc_final: 0.7638 (m-30) REVERT: J 157 LYS cc_start: 0.7404 (ttmt) cc_final: 0.7141 (ttpp) REVERT: J 159 SER cc_start: 0.6238 (t) cc_final: 0.5900 (p) REVERT: J 163 GLU cc_start: 0.6702 (tt0) cc_final: 0.6159 (tp30) REVERT: J 167 GLN cc_start: 0.6877 (mt0) cc_final: 0.6401 (tp40) REVERT: K 27 GLN cc_start: 0.7738 (tp40) cc_final: 0.7260 (pt0) REVERT: K 30 LYS cc_start: 0.7592 (mmmm) cc_final: 0.6951 (mtmt) REVERT: K 42 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8612 (mm-30) REVERT: K 58 ARG cc_start: 0.6896 (mtm-85) cc_final: 0.6685 (mtp85) REVERT: K 66 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7588 (pttt) REVERT: K 79 ARG cc_start: 0.8072 (ppp-140) cc_final: 0.6851 (ttm-80) REVERT: K 103 GLU cc_start: 0.7535 (mp0) cc_final: 0.7010 (mt-10) REVERT: K 144 ILE cc_start: 0.7351 (mt) cc_final: 0.7090 (mt) REVERT: K 158 ASP cc_start: 0.6796 (p0) cc_final: 0.6574 (m-30) REVERT: L 5 LYS cc_start: 0.6922 (tppt) cc_final: 0.6341 (ttpp) REVERT: L 14 LEU cc_start: 0.7379 (tp) cc_final: 0.6940 (tt) REVERT: L 24 LYS cc_start: 0.8396 (tttm) cc_final: 0.7140 (ttmt) REVERT: L 29 MET cc_start: 0.7485 (tpp) cc_final: 0.7223 (ttm) REVERT: L 30 PRO cc_start: 0.8295 (Cg_endo) cc_final: 0.8022 (Cg_exo) REVERT: L 31 LYS cc_start: 0.7579 (mmtm) cc_final: 0.7202 (mtmt) REVERT: L 96 ARG cc_start: 0.3657 (tmt170) cc_final: 0.3431 (ttp-170) REVERT: M 38 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8072 (pttm) REVERT: M 45 LYS cc_start: 0.8132 (mptp) cc_final: 0.7418 (mtmm) REVERT: M 103 GLU cc_start: 0.8295 (pt0) cc_final: 0.7723 (pt0) REVERT: M 121 GLN cc_start: 0.6169 (mm-40) cc_final: 0.5602 (mp10) REVERT: N 22 LEU cc_start: 0.4091 (OUTLIER) cc_final: 0.3529 (mt) REVERT: N 63 LYS cc_start: 0.6041 (ttmt) cc_final: 0.5439 (tptp) REVERT: O 9 LYS cc_start: 0.8152 (mttm) cc_final: 0.7584 (mmtt) REVERT: O 13 GLN cc_start: 0.7919 (mt0) cc_final: 0.7627 (mt0) REVERT: O 19 ARG cc_start: 0.7139 (mtm180) cc_final: 0.6756 (mtp180) REVERT: O 20 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.6535 (mtt180) REVERT: O 25 TRP cc_start: 0.7850 (p90) cc_final: 0.7197 (p90) REVERT: O 38 TYR cc_start: 0.7252 (m-10) cc_final: 0.6916 (m-80) REVERT: O 58 HIS cc_start: 0.6827 (m90) cc_final: 0.6623 (m-70) REVERT: O 92 ILE cc_start: 0.8571 (mt) cc_final: 0.8254 (mm) REVERT: O 96 VAL cc_start: 0.8477 (t) cc_final: 0.8253 (m) REVERT: O 99 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7189 (ttp-110) REVERT: P 50 LYS cc_start: 0.7411 (tmtm) cc_final: 0.6380 (ttmm) REVERT: P 63 LYS cc_start: 0.5705 (mmpt) cc_final: 0.5298 (mmmt) REVERT: P 65 ASP cc_start: 0.8441 (m-30) cc_final: 0.7981 (m-30) REVERT: P 72 TYR cc_start: 0.8006 (t80) cc_final: 0.7433 (t80) REVERT: P 124 MET cc_start: 0.7813 (mmm) cc_final: 0.7569 (mmp) REVERT: P 125 LYS cc_start: 0.6913 (mmmt) cc_final: 0.6548 (mttt) REVERT: P 130 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: P 143 LYS cc_start: 0.7667 (ttpt) cc_final: 0.7397 (tptt) REVERT: Q 15 PHE cc_start: 0.5255 (p90) cc_final: 0.4567 (p90) REVERT: Q 22 LEU cc_start: 0.7586 (tp) cc_final: 0.7324 (mt) REVERT: Q 30 TYR cc_start: 0.6928 (m-10) cc_final: 0.6439 (m-10) REVERT: Q 32 GLN cc_start: 0.7505 (tp40) cc_final: 0.7297 (pt0) REVERT: Q 41 GLN cc_start: 0.7794 (mp10) cc_final: 0.7361 (mp10) REVERT: Q 58 LYS cc_start: 0.6907 (mmtt) cc_final: 0.6344 (mptt) REVERT: Q 72 LYS cc_start: 0.7326 (mttt) cc_final: 0.6463 (ptmt) REVERT: Q 89 MET cc_start: 0.7608 (mtt) cc_final: 0.7402 (ttm) REVERT: Q 93 MET cc_start: 0.6492 (tpp) cc_final: 0.6150 (tpp) REVERT: Q 106 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6592 (tm-30) REVERT: Q 118 GLU cc_start: 0.7243 (tt0) cc_final: 0.7032 (mt-10) REVERT: R 11 GLN cc_start: 0.6010 (mt0) cc_final: 0.5404 (mt0) REVERT: R 18 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7732 (p) REVERT: R 39 LEU cc_start: 0.7938 (mt) cc_final: 0.7600 (tp) REVERT: R 98 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7280 (tppt) REVERT: R 106 LYS cc_start: 0.6938 (ttpm) cc_final: 0.6510 (tttm) REVERT: R 146 ARG cc_start: 0.6028 (mpt90) cc_final: 0.4768 (mtm110) REVERT: S 6 THR cc_start: 0.8335 (p) cc_final: 0.7781 (t) REVERT: S 40 ILE cc_start: 0.7983 (mt) cc_final: 0.7771 (mm) REVERT: S 62 GLN cc_start: 0.6236 (mm-40) cc_final: 0.5621 (mt0) REVERT: S 107 LYS cc_start: 0.6249 (tmmt) cc_final: 0.5554 (ttmm) REVERT: T 16 LEU cc_start: 0.7209 (mt) cc_final: 0.6988 (mp) REVERT: T 23 ARG cc_start: 0.6677 (mtm180) cc_final: 0.6449 (mtp-110) REVERT: T 46 ARG cc_start: 0.7573 (mmt180) cc_final: 0.6466 (mtp180) REVERT: T 54 LYS cc_start: 0.7070 (mttt) cc_final: 0.6148 (mptt) REVERT: T 89 ASP cc_start: 0.6124 (t0) cc_final: 0.5901 (t0) REVERT: T 94 LYS cc_start: 0.6299 (mttp) cc_final: 0.5906 (mmmt) REVERT: T 96 SER cc_start: 0.8819 (p) cc_final: 0.8601 (m) REVERT: T 98 VAL cc_start: 0.8052 (t) cc_final: 0.7804 (m) REVERT: T 123 LEU cc_start: 0.7841 (mt) cc_final: 0.7636 (mm) REVERT: T 127 TRP cc_start: 0.7658 (m-10) cc_final: 0.7301 (m-10) REVERT: T 129 LEU cc_start: 0.7758 (mt) cc_final: 0.7393 (mt) REVERT: U 8 ASP cc_start: 0.6622 (t70) cc_final: 0.6284 (m-30) REVERT: U 88 MET cc_start: 0.6483 (mtm) cc_final: 0.6194 (mtp) REVERT: V 21 ARG cc_start: 0.6319 (ttt90) cc_final: 0.5196 (mmt-90) REVERT: V 27 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7586 (mtp-110) REVERT: V 30 LYS cc_start: 0.6869 (ptmt) cc_final: 0.6470 (mmmt) REVERT: V 41 ARG cc_start: 0.5692 (mtt-85) cc_final: 0.5353 (ttm-80) REVERT: V 44 LYS cc_start: 0.6995 (mptm) cc_final: 0.6248 (mtpt) REVERT: V 62 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6541 (mtt90) REVERT: V 78 ASP cc_start: 0.8951 (m-30) cc_final: 0.8643 (m-30) REVERT: V 93 SER cc_start: 0.6929 (t) cc_final: 0.6627 (t) REVERT: V 114 VAL cc_start: 0.7096 (t) cc_final: 0.6850 (m) REVERT: W 4 ASN cc_start: 0.5780 (OUTLIER) cc_final: 0.5492 (m-40) REVERT: W 27 LYS cc_start: 0.7517 (mmtt) cc_final: 0.7126 (mmtm) REVERT: W 45 ARG cc_start: 0.6991 (mtt180) cc_final: 0.6438 (mtm-85) REVERT: X 13 SER cc_start: 0.8706 (t) cc_final: 0.8295 (m) REVERT: X 41 MET cc_start: 0.8338 (mtm) cc_final: 0.8007 (mtp) REVERT: X 87 GLU cc_start: 0.8120 (tp30) cc_final: 0.7381 (mm-30) REVERT: X 111 MET cc_start: 0.8385 (ptt) cc_final: 0.8026 (ptt) REVERT: Y 29 LYS cc_start: 0.8155 (tttm) cc_final: 0.7816 (ttmm) REVERT: Y 53 GLU cc_start: 0.7670 (pt0) cc_final: 0.6321 (tp30) REVERT: Y 71 ARG cc_start: 0.7496 (tpt170) cc_final: 0.7123 (mmm160) REVERT: Y 88 ASP cc_start: 0.8062 (t0) cc_final: 0.7651 (t70) REVERT: Y 108 LYS cc_start: 0.8564 (mttt) cc_final: 0.7572 (mmtt) REVERT: Y 127 ASN cc_start: 0.7747 (m110) cc_final: 0.7427 (t0) REVERT: Y 129 SER cc_start: 0.8281 (p) cc_final: 0.8074 (p) REVERT: Z 4 THR cc_start: 0.5814 (t) cc_final: 0.5530 (m) REVERT: Z 8 ARG cc_start: 0.7193 (mtt-85) cc_final: 0.6008 (ttt90) REVERT: Z 13 MET cc_start: 0.7276 (ttm) cc_final: 0.6887 (ttm) REVERT: Z 16 ARG cc_start: 0.7347 (mmp-170) cc_final: 0.7073 (mmt180) REVERT: Z 39 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6977 (tm-30) REVERT: Z 42 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7130 (pt0) REVERT: Z 44 LEU cc_start: 0.8497 (tp) cc_final: 0.8237 (tp) REVERT: Z 46 LYS cc_start: 0.7011 (pttp) cc_final: 0.6695 (mmtt) REVERT: Z 47 MET cc_start: 0.6954 (tpp) cc_final: 0.6565 (ttt) REVERT: Z 48 TYR cc_start: 0.6120 (m-80) cc_final: 0.5917 (m-80) REVERT: Z 69 THR cc_start: 0.7957 (t) cc_final: 0.7623 (m) REVERT: Z 102 THR cc_start: 0.6012 (p) cc_final: 0.5653 (p) REVERT: Z 106 GLN cc_start: 0.7886 (mt0) cc_final: 0.7397 (mm110) REVERT: a 60 LYS cc_start: 0.6919 (mmtt) cc_final: 0.6609 (mttt) REVERT: a 61 GLU cc_start: 0.6443 (mm-30) cc_final: 0.6163 (mm-30) REVERT: a 85 ARG cc_start: 0.7450 (mtm110) cc_final: 0.7112 (mtm110) REVERT: a 111 ARG cc_start: 0.5942 (ptt180) cc_final: 0.5089 (ptp-110) REVERT: b 89 ARG cc_start: 0.6884 (mtp-110) cc_final: 0.6459 (mtt90) REVERT: b 93 LYS cc_start: 0.7755 (mttt) cc_final: 0.7475 (mtpt) REVERT: b 94 ASP cc_start: 0.7367 (m-30) cc_final: 0.7002 (m-30) REVERT: c 15 GLU cc_start: 0.7208 (tt0) cc_final: 0.6852 (tp30) REVERT: c 33 MET cc_start: 0.6873 (mtm) cc_final: 0.6302 (mtm) REVERT: c 36 LYS cc_start: 0.5930 (pttm) cc_final: 0.5285 (tptm) REVERT: c 48 SER cc_start: 0.7913 (p) cc_final: 0.7630 (m) REVERT: c 72 ARG cc_start: 0.6738 (mtm180) cc_final: 0.6220 (ttm170) REVERT: c 77 CYS cc_start: 0.7171 (m) cc_final: 0.6931 (m) REVERT: d 27 CYS cc_start: 0.8058 (m) cc_final: 0.7812 (m) REVERT: d 33 GLU cc_start: 0.7837 (tp30) cc_final: 0.7534 (mm-30) REVERT: d 51 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6946 (ptt-90) REVERT: e 8 TRP cc_start: 0.8060 (t-100) cc_final: 0.7853 (t-100) REVERT: e 12 ARG cc_start: 0.7003 (mmt90) cc_final: 0.6787 (mmt90) REVERT: e 13 LYS cc_start: 0.7706 (mttt) cc_final: 0.6692 (mmtm) REVERT: e 38 MET cc_start: 0.8318 (ttm) cc_final: 0.7901 (ttm) REVERT: e 54 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7542 (ttmt) REVERT: f 91 LYS cc_start: 0.8457 (tttt) cc_final: 0.8193 (tppt) REVERT: f 114 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7477 (mtt180) REVERT: f 126 LYS cc_start: 0.6389 (mtmt) cc_final: 0.6120 (pttt) REVERT: g 95 ARG cc_start: 0.5701 (mmm160) cc_final: 0.5368 (tpp-160) REVERT: g 104 LYS cc_start: 0.5762 (mppt) cc_final: 0.5494 (tptt) REVERT: g 140 TYR cc_start: 0.2563 (t80) cc_final: 0.1923 (t80) REVERT: h 15 ASN cc_start: 0.6982 (m-40) cc_final: 0.6722 (m-40) REVERT: h 26 GLN cc_start: 0.7728 (mm110) cc_final: 0.7303 (mp10) REVERT: h 30 MET cc_start: 0.4284 (tmm) cc_final: 0.3542 (mmt) REVERT: h 57 ARG cc_start: 0.7157 (tpp80) cc_final: 0.6704 (mtp85) REVERT: h 89 LEU cc_start: 0.7449 (tp) cc_final: 0.7129 (tt) REVERT: h 106 LYS cc_start: 0.7557 (mttm) cc_final: 0.7169 (mtpp) REVERT: h 107 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: h 119 GLN cc_start: 0.5820 (mm110) cc_final: 0.5467 (pm20) REVERT: h 139 LYS cc_start: 0.5963 (tppp) cc_final: 0.5263 (pttp) REVERT: h 164 ILE cc_start: 0.6929 (mt) cc_final: 0.6559 (mt) REVERT: h 165 ILE cc_start: 0.7562 (pt) cc_final: 0.7343 (mt) REVERT: h 172 LYS cc_start: 0.6785 (mtmt) cc_final: 0.6371 (mmtt) REVERT: h 177 TRP cc_start: 0.7110 (m100) cc_final: 0.6833 (m100) REVERT: h 256 ILE cc_start: 0.7040 (mt) cc_final: 0.6753 (mp) REVERT: h 264 LYS cc_start: 0.5886 (mptt) cc_final: 0.5541 (ttpt) REVERT: n 16 LYS cc_start: 0.7351 (ttmt) cc_final: 0.7090 (ttmm) outliers start: 141 outliers final: 44 residues processed: 1510 average time/residue: 0.8905 time to fit residues: 2144.7935 Evaluate side-chains 1067 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1004 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 277 HIS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain M residue 38 LYS Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 130 GLU Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain W residue 4 ASN Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 38 GLU Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 28 CYS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain d residue 51 ARG Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain h residue 107 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 0.9980 chunk 500 optimal weight: 0.8980 chunk 277 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 337 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 517 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 chunk 385 optimal weight: 3.9990 chunk 599 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 193 HIS C 92 GLN C 99 ASN C 186 ASN C 232 HIS D 272 HIS E 165 ASN E 174 HIS F 112 HIS G 149 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN H 177 GLN I 168 HIS J 22 HIS J 84 ASN J 99 ASN J 165 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN N 55 ASN O 36 GLN P 94 HIS ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS T 87 GLN T 134 GLN V 81 GLN X 24 GLN X 113 HIS Y 46 HIS Y 127 ASN Z 63 HIS Z 94 HIS a 112 ASN b 17 HIS b 43 ASN ** b 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 HIS c 49 HIS c 65 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 84823 Z= 0.174 Angle : 0.661 14.561 123619 Z= 0.341 Chirality : 0.040 0.450 15363 Planarity : 0.004 0.057 8630 Dihedral : 24.207 179.807 35156 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 4.48 % Allowed : 14.05 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.11), residues: 4788 helix: -0.64 (0.12), residues: 1550 sheet: -2.14 (0.15), residues: 876 loop : -1.78 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP h 132 HIS 0.008 0.001 HIS V 85 PHE 0.029 0.002 PHE J 197 TYR 0.018 0.002 TYR Q 123 ARG 0.010 0.001 ARG R 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1105 time to evaluate : 4.336 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: B 6 ASP cc_start: 0.8307 (m-30) cc_final: 0.7527 (p0) REVERT: B 52 LYS cc_start: 0.7436 (tttt) cc_final: 0.6320 (mttp) REVERT: B 73 ASP cc_start: 0.6935 (p0) cc_final: 0.6488 (p0) REVERT: B 111 GLN cc_start: 0.7335 (pm20) cc_final: 0.6888 (pm20) REVERT: B 117 ARG cc_start: 0.6984 (mmt90) cc_final: 0.6420 (mmm160) REVERT: B 135 MET cc_start: 0.6286 (mmm) cc_final: 0.5899 (mmt) REVERT: B 189 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7104 (pt) REVERT: B 196 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6207 (pp20) REVERT: C 27 LYS cc_start: 0.7987 (mttp) cc_final: 0.7481 (mmtt) REVERT: C 77 ASP cc_start: 0.7720 (t70) cc_final: 0.7348 (m-30) REVERT: C 92 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.5860 (mm-40) REVERT: C 112 SER cc_start: 0.8356 (t) cc_final: 0.8075 (p) REVERT: C 115 LYS cc_start: 0.7540 (mtmp) cc_final: 0.7079 (mttp) REVERT: C 195 LYS cc_start: 0.6868 (mmpt) cc_final: 0.6111 (pttm) REVERT: C 198 GLU cc_start: 0.6404 (tt0) cc_final: 0.6044 (tt0) REVERT: C 230 GLU cc_start: 0.7759 (tt0) cc_final: 0.7089 (tp30) REVERT: D 68 ARG cc_start: 0.8034 (tpm170) cc_final: 0.7606 (tpp-160) REVERT: D 72 ASP cc_start: 0.6731 (m-30) cc_final: 0.5519 (m-30) REVERT: D 73 MET cc_start: 0.7421 (mmm) cc_final: 0.7077 (mtm) REVERT: D 90 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7594 (mm-30) REVERT: D 105 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6322 (tp30) REVERT: D 145 LYS cc_start: 0.7898 (mttm) cc_final: 0.7185 (ptpt) REVERT: D 146 GLU cc_start: 0.7658 (pm20) cc_final: 0.6644 (mp0) REVERT: D 250 TYR cc_start: 0.8179 (t80) cc_final: 0.7932 (t80) REVERT: D 277 HIS cc_start: 0.3028 (OUTLIER) cc_final: 0.2108 (p-80) REVERT: E 28 GLU cc_start: 0.7146 (tp30) cc_final: 0.6912 (mm-30) REVERT: E 56 GLN cc_start: 0.5651 (tt0) cc_final: 0.4858 (mm-40) REVERT: E 74 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6563 (pp30) REVERT: E 87 TYR cc_start: 0.4796 (m-80) cc_final: 0.4594 (m-80) REVERT: E 116 ARG cc_start: 0.6651 (mmt90) cc_final: 0.6061 (mtp180) REVERT: E 117 ARG cc_start: 0.7565 (mmm160) cc_final: 0.6658 (mtt180) REVERT: E 119 CYS cc_start: 0.7791 (m) cc_final: 0.7440 (m) REVERT: E 143 ARG cc_start: 0.5086 (ttp80) cc_final: 0.4334 (mmm-85) REVERT: E 178 ARG cc_start: 0.6499 (ptt90) cc_final: 0.5991 (ttm110) REVERT: F 71 LYS cc_start: 0.6758 (ttpt) cc_final: 0.6258 (mtmt) REVERT: F 118 GLU cc_start: 0.7136 (tt0) cc_final: 0.6339 (tm-30) REVERT: F 120 LYS cc_start: 0.7255 (ttmp) cc_final: 0.6924 (tppt) REVERT: F 250 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6839 (mt-10) REVERT: G 25 THR cc_start: 0.7864 (m) cc_final: 0.7572 (t) REVERT: G 47 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7812 (mmtt) REVERT: G 55 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7331 (mtm110) REVERT: G 98 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7049 (mm-30) REVERT: G 106 GLU cc_start: 0.6537 (tt0) cc_final: 0.6140 (tt0) REVERT: G 136 ARG cc_start: 0.6971 (mmm-85) cc_final: 0.6560 (mtm180) REVERT: G 169 ILE cc_start: 0.6227 (OUTLIER) cc_final: 0.5660 (mp) REVERT: G 186 ASN cc_start: 0.7820 (t0) cc_final: 0.7218 (m110) REVERT: G 190 ILE cc_start: 0.7818 (mm) cc_final: 0.7506 (mm) REVERT: G 198 ARG cc_start: 0.7647 (ttm110) cc_final: 0.7228 (ttm-80) REVERT: H 22 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6504 (ttt-90) REVERT: H 30 LYS cc_start: 0.6478 (mmtm) cc_final: 0.5957 (mmtt) REVERT: H 63 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6248 (mtt) REVERT: H 101 ILE cc_start: 0.5475 (OUTLIER) cc_final: 0.4981 (mp) REVERT: H 149 LYS cc_start: 0.6082 (mtmt) cc_final: 0.5280 (mmmt) REVERT: H 154 ARG cc_start: 0.7259 (mtt-85) cc_final: 0.6929 (mtm180) REVERT: H 155 GLN cc_start: 0.5590 (mt0) cc_final: 0.5126 (mm-40) REVERT: H 197 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8122 (mt0) REVERT: I 72 PHE cc_start: 0.6469 (m-80) cc_final: 0.6184 (m-80) REVERT: I 179 LYS cc_start: 0.7015 (tptm) cc_final: 0.6574 (tptp) REVERT: J 8 TRP cc_start: 0.8238 (p-90) cc_final: 0.7870 (p-90) REVERT: J 28 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7940 (mt-10) REVERT: J 92 ARG cc_start: 0.7003 (tmm-80) cc_final: 0.6716 (mtt180) REVERT: J 134 GLU cc_start: 0.6392 (tt0) cc_final: 0.6048 (tp30) REVERT: J 150 ASP cc_start: 0.7745 (m-30) cc_final: 0.7437 (m-30) REVERT: J 159 SER cc_start: 0.5910 (t) cc_final: 0.5594 (p) REVERT: J 163 GLU cc_start: 0.6501 (tt0) cc_final: 0.6064 (tp30) REVERT: J 167 GLN cc_start: 0.6693 (mt0) cc_final: 0.6249 (mm-40) REVERT: K 27 GLN cc_start: 0.7559 (tp40) cc_final: 0.7102 (pt0) REVERT: K 30 LYS cc_start: 0.7345 (mmmm) cc_final: 0.6753 (mtmt) REVERT: K 66 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7578 (pttt) REVERT: K 79 ARG cc_start: 0.7658 (ppp-140) cc_final: 0.6673 (ttm-80) REVERT: K 103 GLU cc_start: 0.7552 (mp0) cc_final: 0.7014 (mt-10) REVERT: K 135 ILE cc_start: 0.7841 (mp) cc_final: 0.7601 (mt) REVERT: K 153 SER cc_start: 0.7906 (t) cc_final: 0.7468 (p) REVERT: K 169 ARG cc_start: 0.5162 (tpt-90) cc_final: 0.4537 (mtm110) REVERT: L 5 LYS cc_start: 0.6540 (tppt) cc_final: 0.6153 (ttpp) REVERT: L 30 PRO cc_start: 0.8090 (Cg_endo) cc_final: 0.7802 (Cg_exo) REVERT: L 31 LYS cc_start: 0.7720 (mmtm) cc_final: 0.7476 (mmmm) REVERT: L 74 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6250 (tp30) REVERT: M 45 LYS cc_start: 0.8117 (mptp) cc_final: 0.7389 (mtmm) REVERT: M 49 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6482 (mt-10) REVERT: M 84 ARG cc_start: 0.7313 (mtt90) cc_final: 0.6969 (mtm-85) REVERT: M 93 LEU cc_start: 0.8285 (mt) cc_final: 0.7781 (mm) REVERT: M 97 ARG cc_start: 0.7858 (ttp-110) cc_final: 0.7377 (ttp-170) REVERT: M 103 GLU cc_start: 0.8027 (pt0) cc_final: 0.7592 (pt0) REVERT: M 104 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7402 (tttm) REVERT: M 108 ASN cc_start: 0.7502 (p0) cc_final: 0.7093 (p0) REVERT: M 121 GLN cc_start: 0.6227 (mm-40) cc_final: 0.5756 (mp10) REVERT: N 63 LYS cc_start: 0.5993 (ttmt) cc_final: 0.5518 (tptp) REVERT: N 103 VAL cc_start: 0.6678 (OUTLIER) cc_final: 0.6421 (t) REVERT: O 9 LYS cc_start: 0.7909 (mttm) cc_final: 0.7514 (mmtt) REVERT: O 19 ARG cc_start: 0.6998 (mtm180) cc_final: 0.6726 (mtp180) REVERT: O 20 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6515 (mtt180) REVERT: O 38 TYR cc_start: 0.7002 (m-10) cc_final: 0.6650 (m-80) REVERT: O 89 TYR cc_start: 0.7685 (t80) cc_final: 0.7353 (t80) REVERT: O 140 LYS cc_start: 0.7987 (tttm) cc_final: 0.7339 (pttm) REVERT: P 50 LYS cc_start: 0.7478 (tmtm) cc_final: 0.6546 (ttmt) REVERT: P 63 LYS cc_start: 0.5610 (mmpt) cc_final: 0.5328 (mmmt) REVERT: P 65 ASP cc_start: 0.8295 (m-30) cc_final: 0.7884 (m-30) REVERT: P 72 TYR cc_start: 0.8005 (t80) cc_final: 0.7731 (t80) REVERT: P 96 LYS cc_start: 0.7636 (mtpt) cc_final: 0.6827 (mmtt) REVERT: P 125 LYS cc_start: 0.6686 (mmmt) cc_final: 0.6381 (mtmt) REVERT: P 149 ARG cc_start: 0.7692 (ttt-90) cc_final: 0.7409 (ttt90) REVERT: Q 15 PHE cc_start: 0.5426 (p90) cc_final: 0.4971 (p90) REVERT: Q 58 LYS cc_start: 0.6279 (mmtt) cc_final: 0.5836 (mptt) REVERT: Q 62 LYS cc_start: 0.5989 (mtpm) cc_final: 0.5190 (mmtm) REVERT: Q 72 LYS cc_start: 0.7132 (mttt) cc_final: 0.6006 (ptmt) REVERT: Q 93 MET cc_start: 0.6687 (tpp) cc_final: 0.6285 (ttp) REVERT: Q 108 LYS cc_start: 0.6994 (ptpt) cc_final: 0.6311 (mmtm) REVERT: Q 118 GLU cc_start: 0.7259 (tt0) cc_final: 0.6919 (mt-10) REVERT: R 11 GLN cc_start: 0.5872 (mt0) cc_final: 0.5449 (mt0) REVERT: R 18 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7584 (p) REVERT: R 39 LEU cc_start: 0.7660 (mt) cc_final: 0.7327 (tp) REVERT: R 98 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7321 (tppt) REVERT: R 106 LYS cc_start: 0.6886 (ttpm) cc_final: 0.6515 (tttm) REVERT: R 146 ARG cc_start: 0.5524 (mpt90) cc_final: 0.4666 (mtm110) REVERT: S 6 THR cc_start: 0.8376 (p) cc_final: 0.7866 (t) REVERT: S 11 LYS cc_start: 0.7774 (mttt) cc_final: 0.7350 (mmtt) REVERT: S 37 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6444 (mm-30) REVERT: S 62 GLN cc_start: 0.6288 (mm-40) cc_final: 0.5689 (tt0) REVERT: S 63 ARG cc_start: 0.5792 (mmp80) cc_final: 0.5303 (tpm170) REVERT: S 93 GLN cc_start: 0.6285 (mt0) cc_final: 0.5494 (tp40) REVERT: S 105 MET cc_start: 0.5731 (ptm) cc_final: 0.5477 (tmm) REVERT: S 107 LYS cc_start: 0.5519 (tmmt) cc_final: 0.5082 (ttmm) REVERT: S 130 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.7201 (p) REVERT: T 46 ARG cc_start: 0.7269 (mmt180) cc_final: 0.6477 (tpt90) REVERT: T 54 LYS cc_start: 0.7052 (mttt) cc_final: 0.6118 (mptt) REVERT: T 92 ASP cc_start: 0.7664 (p0) cc_final: 0.7255 (p0) REVERT: T 94 LYS cc_start: 0.6119 (mttp) cc_final: 0.5842 (ptmt) REVERT: T 123 LEU cc_start: 0.7904 (mt) cc_final: 0.7659 (mm) REVERT: T 126 PHE cc_start: 0.6732 (t80) cc_final: 0.6406 (t80) REVERT: T 129 LEU cc_start: 0.7647 (mt) cc_final: 0.7440 (mt) REVERT: U 8 ASP cc_start: 0.6900 (t70) cc_final: 0.6595 (m-30) REVERT: U 88 MET cc_start: 0.6330 (mtm) cc_final: 0.6095 (mtp) REVERT: U 126 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: U 133 ARG cc_start: 0.7192 (mtp180) cc_final: 0.6817 (mtm-85) REVERT: V 21 ARG cc_start: 0.6281 (ttt90) cc_final: 0.5324 (mmt-90) REVERT: V 27 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7479 (mtp-110) REVERT: V 30 LYS cc_start: 0.7291 (ptmt) cc_final: 0.6791 (mmmt) REVERT: V 44 LYS cc_start: 0.6591 (mptm) cc_final: 0.6145 (mtpt) REVERT: V 65 THR cc_start: 0.7038 (OUTLIER) cc_final: 0.6799 (t) REVERT: V 68 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7217 (t) REVERT: V 78 ASP cc_start: 0.8923 (m-30) cc_final: 0.8709 (m-30) REVERT: W 1 MET cc_start: 0.6165 (ttp) cc_final: 0.5937 (ttp) REVERT: W 27 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7229 (mmtm) REVERT: W 45 ARG cc_start: 0.6829 (mtt180) cc_final: 0.6425 (mtm-85) REVERT: X 13 SER cc_start: 0.8615 (t) cc_final: 0.8309 (m) REVERT: X 41 MET cc_start: 0.8292 (mtm) cc_final: 0.8010 (mtp) REVERT: X 87 GLU cc_start: 0.8198 (tp30) cc_final: 0.7753 (mm-30) REVERT: X 115 GLU cc_start: 0.8466 (tt0) cc_final: 0.7555 (tp30) REVERT: Y 11 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7597 (ttm110) REVERT: Y 37 LYS cc_start: 0.7278 (tptt) cc_final: 0.6831 (tmtt) REVERT: Y 53 GLU cc_start: 0.7818 (pt0) cc_final: 0.6461 (tp30) REVERT: Y 71 ARG cc_start: 0.7550 (tpt170) cc_final: 0.7277 (mmm160) REVERT: Y 95 GLU cc_start: 0.7798 (tt0) cc_final: 0.7259 (mp0) REVERT: Z 4 THR cc_start: 0.6054 (t) cc_final: 0.5788 (m) REVERT: Z 8 ARG cc_start: 0.7222 (mtt-85) cc_final: 0.5936 (ttt90) REVERT: Z 13 MET cc_start: 0.7326 (ttm) cc_final: 0.6882 (ttm) REVERT: Z 16 ARG cc_start: 0.7639 (mmp-170) cc_final: 0.7277 (mmt180) REVERT: Z 39 GLU cc_start: 0.7686 (mt-10) cc_final: 0.6764 (mp0) REVERT: Z 42 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7100 (pt0) REVERT: Z 44 LEU cc_start: 0.8342 (tp) cc_final: 0.8072 (tp) REVERT: Z 47 MET cc_start: 0.6939 (tpp) cc_final: 0.6593 (ttt) REVERT: Z 48 TYR cc_start: 0.5917 (m-80) cc_final: 0.5556 (m-80) REVERT: Z 61 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.7390 (mmm-85) REVERT: Z 102 THR cc_start: 0.6070 (p) cc_final: 0.5839 (p) REVERT: Z 106 GLN cc_start: 0.7857 (mt0) cc_final: 0.7476 (mm110) REVERT: a 60 LYS cc_start: 0.6875 (mmtt) cc_final: 0.6381 (mttt) REVERT: a 61 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6288 (mm-30) REVERT: b 10 ARG cc_start: 0.8405 (ptm160) cc_final: 0.8145 (ptp-170) REVERT: b 89 ARG cc_start: 0.6969 (mtp-110) cc_final: 0.6577 (mtt180) REVERT: b 93 LYS cc_start: 0.7656 (mttt) cc_final: 0.7353 (mtpt) REVERT: b 94 ASP cc_start: 0.6961 (m-30) cc_final: 0.6653 (m-30) REVERT: c 26 GLN cc_start: 0.7013 (tt0) cc_final: 0.6549 (mt0) REVERT: c 36 LYS cc_start: 0.5612 (pttm) cc_final: 0.5091 (tptp) REVERT: c 72 ARG cc_start: 0.6368 (mtm180) cc_final: 0.6053 (ttm170) REVERT: d 33 GLU cc_start: 0.7510 (tp30) cc_final: 0.7231 (mm-30) REVERT: e 13 LYS cc_start: 0.8036 (mttt) cc_final: 0.7150 (mmtm) REVERT: e 38 MET cc_start: 0.7747 (ttm) cc_final: 0.7303 (ttm) REVERT: f 126 LYS cc_start: 0.6358 (mtmt) cc_final: 0.6075 (pttt) REVERT: g 95 ARG cc_start: 0.5826 (mmm160) cc_final: 0.5003 (mpt180) REVERT: g 114 ILE cc_start: 0.4730 (OUTLIER) cc_final: 0.4525 (tp) REVERT: g 140 TYR cc_start: 0.2625 (t80) cc_final: 0.2337 (t80) REVERT: h 15 ASN cc_start: 0.6781 (m-40) cc_final: 0.6539 (m-40) REVERT: h 20 GLN cc_start: 0.5558 (tp40) cc_final: 0.5199 (tm-30) REVERT: h 26 GLN cc_start: 0.7783 (mm110) cc_final: 0.7449 (mp10) REVERT: h 38 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.6869 (mmtp) REVERT: h 89 LEU cc_start: 0.7419 (tp) cc_final: 0.7207 (tt) REVERT: h 107 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6987 (m-30) REVERT: h 152 SER cc_start: 0.5553 (OUTLIER) cc_final: 0.5207 (m) REVERT: h 172 LYS cc_start: 0.6677 (mtmt) cc_final: 0.6300 (mptt) REVERT: h 217 MET cc_start: 0.5235 (mtt) cc_final: 0.4680 (ttm) REVERT: h 228 TYR cc_start: 0.6695 (p90) cc_final: 0.6230 (p90) REVERT: h 246 TYR cc_start: 0.6532 (t80) cc_final: 0.5960 (t80) REVERT: h 256 ILE cc_start: 0.6880 (mt) cc_final: 0.6551 (mp) REVERT: h 264 LYS cc_start: 0.6235 (mptt) cc_final: 0.5579 (ttpt) REVERT: h 285 GLN cc_start: 0.6119 (tp40) cc_final: 0.5796 (tp40) REVERT: n 1 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.6264 (tmm) REVERT: n 16 LYS cc_start: 0.7063 (ttmt) cc_final: 0.6736 (ttmm) REVERT: n 21 ARG cc_start: 0.7082 (ttt90) cc_final: 0.6618 (mtp180) outliers start: 188 outliers final: 98 residues processed: 1224 average time/residue: 0.8648 time to fit residues: 1711.7061 Evaluate side-chains 1045 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 927 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 277 HIS Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 90 LYS Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 126 GLN Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 84 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain X residue 24 GLN Chi-restraints excluded: chain X residue 49 GLU Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 29 CYS Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain g residue 114 ILE Chi-restraints excluded: chain h residue 38 LYS Chi-restraints excluded: chain h residue 88 ARG Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 152 SER Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain n residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 8.9990 chunk 186 optimal weight: 0.6980 chunk 498 optimal weight: 3.9990 chunk 408 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 600 optimal weight: 0.5980 chunk 648 optimal weight: 10.0000 chunk 534 optimal weight: 0.5980 chunk 595 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 chunk 481 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 HIS D 277 HIS F 201 HIS G 31 ASN G 149 GLN H 177 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 111 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 73 ASN M 100 ASN O 13 GLN Q 32 GLN Q 53 GLN Q 104 GLN S 118 GLN T 17 ASN T 19 ASN T 134 GLN U 85 ASN V 28 ASN Z 15 ASN Z 63 HIS d 26 GLN g 139 HIS h 143 GLN h 222 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 84823 Z= 0.147 Angle : 0.578 15.044 123619 Z= 0.299 Chirality : 0.037 0.297 15363 Planarity : 0.004 0.062 8630 Dihedral : 23.948 179.795 35092 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 4.58 % Allowed : 16.20 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4788 helix: 0.23 (0.13), residues: 1566 sheet: -1.72 (0.16), residues: 868 loop : -1.52 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP h 132 HIS 0.009 0.001 HIS O 58 PHE 0.027 0.002 PHE J 197 TYR 0.019 0.001 TYR h 140 ARG 0.007 0.000 ARG M 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1011 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 ASP cc_start: 0.8296 (m-30) cc_final: 0.7521 (p0) REVERT: B 52 LYS cc_start: 0.7270 (tttt) cc_final: 0.6246 (mttp) REVERT: B 73 ASP cc_start: 0.6666 (p0) cc_final: 0.6314 (p0) REVERT: B 111 GLN cc_start: 0.7202 (pm20) cc_final: 0.6822 (pm20) REVERT: B 117 ARG cc_start: 0.7003 (mmt90) cc_final: 0.6434 (mmm160) REVERT: B 135 MET cc_start: 0.6284 (mmm) cc_final: 0.5882 (mmt) REVERT: B 189 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7224 (pt) REVERT: C 27 LYS cc_start: 0.7965 (mttp) cc_final: 0.7463 (mmtt) REVERT: C 46 LYS cc_start: 0.8409 (mmmm) cc_final: 0.7571 (mtpt) REVERT: C 82 ARG cc_start: 0.7790 (ttm110) cc_final: 0.6624 (mtm-85) REVERT: C 103 MET cc_start: 0.7182 (tmm) cc_final: 0.6687 (tmm) REVERT: C 115 LYS cc_start: 0.7492 (mtmp) cc_final: 0.7050 (mttp) REVERT: C 195 LYS cc_start: 0.6882 (mmpt) cc_final: 0.6178 (pttm) REVERT: C 230 GLU cc_start: 0.7686 (tt0) cc_final: 0.7067 (tp30) REVERT: D 63 VAL cc_start: 0.7919 (t) cc_final: 0.7695 (m) REVERT: D 68 ARG cc_start: 0.8018 (tpm170) cc_final: 0.7612 (tpp-160) REVERT: D 72 ASP cc_start: 0.6810 (m-30) cc_final: 0.5618 (m-30) REVERT: D 73 MET cc_start: 0.7444 (mmm) cc_final: 0.7193 (mtm) REVERT: D 105 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6237 (tp30) REVERT: D 145 LYS cc_start: 0.7903 (mttm) cc_final: 0.7072 (ptpt) REVERT: D 146 GLU cc_start: 0.7518 (pm20) cc_final: 0.6812 (mm-30) REVERT: D 176 LYS cc_start: 0.7085 (mmmt) cc_final: 0.6704 (mtpt) REVERT: D 180 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7791 (m) REVERT: D 277 HIS cc_start: 0.2820 (OUTLIER) cc_final: 0.2224 (p90) REVERT: E 28 GLU cc_start: 0.7089 (tp30) cc_final: 0.6553 (mm-30) REVERT: E 56 GLN cc_start: 0.5485 (tt0) cc_final: 0.4848 (mm-40) REVERT: E 68 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6313 (pt0) REVERT: E 74 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6508 (tm-30) REVERT: E 87 TYR cc_start: 0.5150 (m-80) cc_final: 0.4591 (m-80) REVERT: E 116 ARG cc_start: 0.6469 (mmt90) cc_final: 0.5835 (mtp180) REVERT: E 117 ARG cc_start: 0.7560 (mmm160) cc_final: 0.6678 (mtt-85) REVERT: E 119 CYS cc_start: 0.7835 (m) cc_final: 0.7497 (m) REVERT: E 143 ARG cc_start: 0.5193 (ttp80) cc_final: 0.4362 (mmm-85) REVERT: E 178 ARG cc_start: 0.6355 (ptt90) cc_final: 0.5943 (ttp-110) REVERT: F 19 MET cc_start: 0.8509 (mtt) cc_final: 0.8295 (mtt) REVERT: F 115 THR cc_start: 0.7267 (OUTLIER) cc_final: 0.7010 (t) REVERT: F 118 GLU cc_start: 0.6929 (tt0) cc_final: 0.6234 (tp30) REVERT: F 120 LYS cc_start: 0.7417 (ttmp) cc_final: 0.7061 (tppt) REVERT: F 156 MET cc_start: 0.4754 (OUTLIER) cc_final: 0.4539 (mtt) REVERT: F 198 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7864 (ttt-90) REVERT: F 199 GLU cc_start: 0.7294 (tt0) cc_final: 0.6828 (tt0) REVERT: G 37 ASP cc_start: 0.7488 (m-30) cc_final: 0.7275 (m-30) REVERT: G 47 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7755 (mmtt) REVERT: G 55 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7248 (mtm110) REVERT: G 76 MET cc_start: 0.8071 (mmm) cc_final: 0.7321 (tpp) REVERT: G 98 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6972 (mm-30) REVERT: G 106 GLU cc_start: 0.7033 (tt0) cc_final: 0.6618 (tt0) REVERT: G 198 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7447 (ttm-80) REVERT: H 1 MET cc_start: 0.5044 (ttp) cc_final: 0.4520 (tmm) REVERT: H 4 ASN cc_start: 0.5385 (t0) cc_final: 0.4995 (t0) REVERT: H 13 GLN cc_start: 0.5850 (pt0) cc_final: 0.5418 (pm20) REVERT: H 22 ARG cc_start: 0.6985 (mtm110) cc_final: 0.6433 (ttt-90) REVERT: H 30 LYS cc_start: 0.6505 (mmtm) cc_final: 0.5461 (ptmt) REVERT: H 59 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7287 (mp10) REVERT: H 63 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6346 (mtp) REVERT: H 149 LYS cc_start: 0.6101 (mtmt) cc_final: 0.5255 (mmmt) REVERT: H 154 ARG cc_start: 0.7618 (mtt-85) cc_final: 0.7075 (mtm180) REVERT: H 155 GLN cc_start: 0.5581 (mt0) cc_final: 0.5156 (mm-40) REVERT: H 197 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7847 (mt0) REVERT: H 217 MET cc_start: 0.4941 (mmm) cc_final: 0.4704 (mmm) REVERT: I 8 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6307 (tt) REVERT: I 169 LYS cc_start: 0.5904 (mttt) cc_final: 0.5673 (mtpp) REVERT: I 179 LYS cc_start: 0.7125 (tptm) cc_final: 0.6743 (tptp) REVERT: J 8 TRP cc_start: 0.8174 (p-90) cc_final: 0.7804 (p-90) REVERT: J 92 ARG cc_start: 0.6971 (tmm-80) cc_final: 0.6682 (ptp-170) REVERT: J 134 GLU cc_start: 0.6287 (tt0) cc_final: 0.5904 (mm-30) REVERT: J 150 ASP cc_start: 0.7770 (m-30) cc_final: 0.7461 (m-30) REVERT: J 151 GLU cc_start: 0.6526 (mm-30) cc_final: 0.6309 (mm-30) REVERT: J 159 SER cc_start: 0.5797 (t) cc_final: 0.5582 (p) REVERT: J 167 GLN cc_start: 0.6848 (mt0) cc_final: 0.6642 (mt0) REVERT: K 27 GLN cc_start: 0.7570 (tp40) cc_final: 0.7112 (pt0) REVERT: K 66 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7606 (pttt) REVERT: K 79 ARG cc_start: 0.7720 (ppp-140) cc_final: 0.6744 (ttm-80) REVERT: K 103 GLU cc_start: 0.7566 (mp0) cc_final: 0.7006 (mt-10) REVERT: K 135 ILE cc_start: 0.7914 (mp) cc_final: 0.7667 (mt) REVERT: K 153 SER cc_start: 0.7886 (t) cc_final: 0.7520 (p) REVERT: K 154 GLN cc_start: 0.7951 (tt0) cc_final: 0.7736 (tt0) REVERT: L 5 LYS cc_start: 0.6451 (tppt) cc_final: 0.5993 (ttpp) REVERT: L 13 GLU cc_start: 0.7549 (tt0) cc_final: 0.7296 (tm-30) REVERT: L 31 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7174 (mtmt) REVERT: L 74 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6412 (tp30) REVERT: L 77 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.6072 (tt0) REVERT: M 45 LYS cc_start: 0.8175 (mptp) cc_final: 0.7370 (mtmm) REVERT: M 48 LYS cc_start: 0.7420 (pptt) cc_final: 0.6873 (mttt) REVERT: M 49 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6470 (mt-10) REVERT: M 84 ARG cc_start: 0.7216 (mtt90) cc_final: 0.6924 (ttm-80) REVERT: M 93 LEU cc_start: 0.8339 (mt) cc_final: 0.7876 (mm) REVERT: M 103 GLU cc_start: 0.7929 (pt0) cc_final: 0.7358 (pt0) REVERT: M 108 ASN cc_start: 0.7143 (p0) cc_final: 0.6628 (p0) REVERT: M 121 GLN cc_start: 0.6242 (mm-40) cc_final: 0.5795 (mp10) REVERT: N 23 LYS cc_start: 0.6223 (mttt) cc_final: 0.5522 (mtmt) REVERT: N 28 HIS cc_start: 0.6640 (m90) cc_final: 0.6439 (m170) REVERT: N 63 LYS cc_start: 0.5939 (ttmt) cc_final: 0.5532 (tptp) REVERT: O 19 ARG cc_start: 0.6949 (mtm180) cc_final: 0.6706 (mtp180) REVERT: O 38 TYR cc_start: 0.6805 (m-10) cc_final: 0.6551 (m-80) REVERT: O 58 HIS cc_start: 0.6055 (m-70) cc_final: 0.5832 (m170) REVERT: O 140 LYS cc_start: 0.7908 (tttm) cc_final: 0.7306 (ttmm) REVERT: P 50 LYS cc_start: 0.7187 (tmtm) cc_final: 0.6142 (ttmt) REVERT: P 51 GLU cc_start: 0.7845 (tp30) cc_final: 0.7565 (tp30) REVERT: P 63 LYS cc_start: 0.5528 (mmpt) cc_final: 0.5282 (mmmt) REVERT: P 65 ASP cc_start: 0.8355 (m-30) cc_final: 0.7912 (m-30) REVERT: P 125 LYS cc_start: 0.6552 (mmmt) cc_final: 0.6128 (mtmt) REVERT: P 128 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7111 (mmt-90) REVERT: P 135 ILE cc_start: 0.8283 (mt) cc_final: 0.8069 (mm) REVERT: Q 15 PHE cc_start: 0.5629 (p90) cc_final: 0.4789 (p90) REVERT: Q 22 LEU cc_start: 0.7345 (tp) cc_final: 0.6718 (mp) REVERT: Q 58 LYS cc_start: 0.6230 (mmtt) cc_final: 0.5744 (mptt) REVERT: Q 62 LYS cc_start: 0.5986 (mtpm) cc_final: 0.5177 (mmtm) REVERT: Q 72 LYS cc_start: 0.6950 (mttt) cc_final: 0.6102 (ptmt) REVERT: Q 89 MET cc_start: 0.7422 (ttm) cc_final: 0.7192 (ttm) REVERT: Q 93 MET cc_start: 0.6919 (tpp) cc_final: 0.6614 (mmm) REVERT: Q 94 VAL cc_start: 0.7355 (t) cc_final: 0.6914 (p) REVERT: Q 108 LYS cc_start: 0.6953 (ptpt) cc_final: 0.6526 (mmtm) REVERT: Q 118 GLU cc_start: 0.7231 (tt0) cc_final: 0.6889 (mt-10) REVERT: R 11 GLN cc_start: 0.5894 (mt0) cc_final: 0.5468 (mt0) REVERT: R 18 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7377 (p) REVERT: R 98 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7238 (tppt) REVERT: R 106 LYS cc_start: 0.6996 (ttpm) cc_final: 0.6637 (tttm) REVERT: R 146 ARG cc_start: 0.5559 (mpt90) cc_final: 0.4525 (mtm110) REVERT: S 6 THR cc_start: 0.8361 (p) cc_final: 0.7851 (t) REVERT: S 11 LYS cc_start: 0.7762 (mttt) cc_final: 0.7292 (mmtt) REVERT: S 37 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6681 (mm-30) REVERT: S 93 GLN cc_start: 0.6265 (mt0) cc_final: 0.5540 (tp40) REVERT: S 107 LYS cc_start: 0.5692 (tmmt) cc_final: 0.5238 (ttmm) REVERT: S 118 GLN cc_start: 0.6417 (tt0) cc_final: 0.5391 (mm110) REVERT: S 126 MET cc_start: 0.6544 (ptp) cc_final: 0.6308 (ptp) REVERT: S 130 THR cc_start: 0.7587 (m) cc_final: 0.7249 (p) REVERT: T 7 GLU cc_start: 0.6082 (mp0) cc_final: 0.5338 (pm20) REVERT: T 46 ARG cc_start: 0.7247 (mmt180) cc_final: 0.6367 (tpt90) REVERT: T 54 LYS cc_start: 0.7103 (mttt) cc_final: 0.6096 (mptt) REVERT: T 63 GLU cc_start: 0.7312 (mp0) cc_final: 0.6986 (mp0) REVERT: T 94 LYS cc_start: 0.6074 (mttp) cc_final: 0.5852 (mmmt) REVERT: T 126 PHE cc_start: 0.6836 (t80) cc_final: 0.6586 (t80) REVERT: U 8 ASP cc_start: 0.6796 (t70) cc_final: 0.6477 (m-30) REVERT: U 108 GLU cc_start: 0.7454 (tt0) cc_final: 0.6994 (mt-10) REVERT: U 133 ARG cc_start: 0.7136 (mtp180) cc_final: 0.6736 (mtm-85) REVERT: V 20 ILE cc_start: 0.7145 (tt) cc_final: 0.6176 (mm) REVERT: V 21 ARG cc_start: 0.6173 (ttt90) cc_final: 0.5408 (mmt-90) REVERT: V 30 LYS cc_start: 0.7111 (ptmt) cc_final: 0.6771 (mmmt) REVERT: V 44 LYS cc_start: 0.6459 (mptm) cc_final: 0.5963 (mtpt) REVERT: V 62 ARG cc_start: 0.7518 (ttm110) cc_final: 0.7112 (mtt90) REVERT: V 65 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6829 (t) REVERT: V 78 ASP cc_start: 0.8939 (m-30) cc_final: 0.8597 (m-30) REVERT: W 45 ARG cc_start: 0.6932 (mtt180) cc_final: 0.6568 (mtm-85) REVERT: X 13 SER cc_start: 0.8553 (t) cc_final: 0.8242 (m) REVERT: X 87 GLU cc_start: 0.8142 (tp30) cc_final: 0.7739 (mm-30) REVERT: X 90 GLN cc_start: 0.8293 (pt0) cc_final: 0.7872 (pt0) REVERT: X 115 GLU cc_start: 0.8388 (tt0) cc_final: 0.7580 (tp30) REVERT: X 119 LYS cc_start: 0.7676 (mttt) cc_final: 0.7359 (mtpt) REVERT: Y 11 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7440 (ttp-110) REVERT: Y 37 LYS cc_start: 0.7582 (tptt) cc_final: 0.7072 (tmtt) REVERT: Y 53 GLU cc_start: 0.7876 (pt0) cc_final: 0.6444 (tp30) REVERT: Y 95 GLU cc_start: 0.7794 (tt0) cc_final: 0.7407 (tt0) REVERT: Z 4 THR cc_start: 0.6062 (t) cc_final: 0.5781 (m) REVERT: Z 8 ARG cc_start: 0.7222 (mtt-85) cc_final: 0.5904 (ttt90) REVERT: Z 13 MET cc_start: 0.7215 (ttm) cc_final: 0.6811 (ttm) REVERT: Z 16 ARG cc_start: 0.7573 (mmp-170) cc_final: 0.7119 (mmt180) REVERT: Z 22 GLN cc_start: 0.8649 (pt0) cc_final: 0.8191 (pt0) REVERT: Z 39 GLU cc_start: 0.7695 (mt-10) cc_final: 0.6715 (mp0) REVERT: Z 42 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7079 (pt0) REVERT: Z 44 LEU cc_start: 0.8302 (tp) cc_final: 0.8102 (tp) REVERT: Z 48 TYR cc_start: 0.6123 (m-80) cc_final: 0.5679 (m-80) REVERT: Z 61 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7275 (mmm-85) REVERT: Z 102 THR cc_start: 0.6073 (p) cc_final: 0.5853 (p) REVERT: Z 106 GLN cc_start: 0.7792 (mt0) cc_final: 0.7402 (mm110) REVERT: a 51 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.6037 (t0) REVERT: a 60 LYS cc_start: 0.6816 (mmtt) cc_final: 0.6560 (mttt) REVERT: a 61 GLU cc_start: 0.6505 (mm-30) cc_final: 0.6245 (mm-30) REVERT: a 92 LEU cc_start: 0.8209 (tp) cc_final: 0.7954 (tp) REVERT: b 44 ILE cc_start: 0.5633 (OUTLIER) cc_final: 0.5412 (pp) REVERT: b 89 ARG cc_start: 0.6918 (mtp-110) cc_final: 0.6491 (mtt90) REVERT: b 93 LYS cc_start: 0.7705 (mttt) cc_final: 0.7407 (mtpt) REVERT: b 94 ASP cc_start: 0.6952 (m-30) cc_final: 0.6692 (m-30) REVERT: c 26 GLN cc_start: 0.6969 (tt0) cc_final: 0.6534 (mt0) REVERT: c 36 LYS cc_start: 0.5650 (pttm) cc_final: 0.5102 (tptp) REVERT: c 72 ARG cc_start: 0.6395 (mtm180) cc_final: 0.5994 (ttm170) REVERT: d 13 ARG cc_start: 0.7151 (ttm170) cc_final: 0.6535 (mtt180) REVERT: d 35 MET cc_start: 0.5895 (mmm) cc_final: 0.5640 (mmm) REVERT: d 57 THR cc_start: 0.7888 (m) cc_final: 0.7683 (m) REVERT: e 8 TRP cc_start: 0.8047 (t-100) cc_final: 0.7504 (t-100) REVERT: e 13 LYS cc_start: 0.7964 (mttt) cc_final: 0.7060 (mmtm) REVERT: e 38 MET cc_start: 0.7637 (ttm) cc_final: 0.7222 (ttm) REVERT: e 48 LYS cc_start: 0.7585 (tppp) cc_final: 0.7178 (ttpp) REVERT: f 96 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7677 (mm-30) REVERT: f 109 MET cc_start: 0.7905 (ttp) cc_final: 0.7655 (tmm) REVERT: f 126 LYS cc_start: 0.6364 (mtmt) cc_final: 0.6075 (pttt) REVERT: g 95 ARG cc_start: 0.5911 (mmm160) cc_final: 0.5520 (tpp80) REVERT: g 132 MET cc_start: 0.4468 (ttm) cc_final: 0.4238 (ttm) REVERT: h 15 ASN cc_start: 0.6898 (m-40) cc_final: 0.6639 (m-40) REVERT: h 20 GLN cc_start: 0.5350 (tp40) cc_final: 0.5018 (tm-30) REVERT: h 26 GLN cc_start: 0.7650 (mm110) cc_final: 0.7222 (mm110) REVERT: h 30 MET cc_start: 0.4431 (tmm) cc_final: 0.3663 (mmt) REVERT: h 38 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6667 (mmtp) REVERT: h 57 ARG cc_start: 0.7158 (tpp80) cc_final: 0.6672 (mmm-85) REVERT: h 107 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: h 172 LYS cc_start: 0.6457 (mtmt) cc_final: 0.6257 (mptt) REVERT: h 217 MET cc_start: 0.5125 (mtt) cc_final: 0.4625 (ttm) REVERT: h 228 TYR cc_start: 0.6666 (p90) cc_final: 0.6264 (p90) REVERT: h 246 TYR cc_start: 0.6599 (t80) cc_final: 0.5970 (t80) REVERT: h 264 LYS cc_start: 0.6306 (mptt) cc_final: 0.5663 (ttpt) REVERT: h 285 GLN cc_start: 0.6219 (tp40) cc_final: 0.5973 (tp40) REVERT: n 1 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.6181 (tmm) REVERT: n 15 ARG cc_start: 0.7089 (ttp-170) cc_final: 0.6764 (ttp-170) REVERT: n 21 ARG cc_start: 0.7057 (ttt90) cc_final: 0.6577 (mtp180) outliers start: 192 outliers final: 112 residues processed: 1130 average time/residue: 0.8354 time to fit residues: 1545.6664 Evaluate side-chains 1043 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 912 time to evaluate : 4.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 277 HIS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 41 ARG Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 84 ILE Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain X residue 49 GLU Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain h residue 38 LYS Chi-restraints excluded: chain h residue 88 ARG Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain n residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 0.9980 chunk 451 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 403 optimal weight: 2.9990 chunk 602 optimal weight: 9.9990 chunk 637 optimal weight: 1.9990 chunk 314 optimal weight: 6.9990 chunk 571 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 GLN F 17 HIS F 36 HIS J 84 ASN J 116 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN O 58 HIS O 62 GLN P 32 HIS W 82 ASN X 15 ASN X 24 GLN Z 63 HIS h 143 GLN h 187 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 84823 Z= 0.222 Angle : 0.610 14.655 123619 Z= 0.311 Chirality : 0.039 0.308 15363 Planarity : 0.004 0.064 8630 Dihedral : 23.900 179.660 35087 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 5.82 % Allowed : 17.22 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4788 helix: 0.34 (0.13), residues: 1568 sheet: -1.50 (0.16), residues: 858 loop : -1.44 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 132 HIS 0.007 0.001 HIS L 28 PHE 0.023 0.002 PHE J 197 TYR 0.019 0.002 TYR L 78 ARG 0.006 0.001 ARG M 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 934 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 ASP cc_start: 0.8318 (m-30) cc_final: 0.7506 (p0) REVERT: B 52 LYS cc_start: 0.7514 (tttt) cc_final: 0.6410 (mttp) REVERT: B 73 ASP cc_start: 0.6788 (p0) cc_final: 0.6510 (p0) REVERT: B 117 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6502 (mmm160) REVERT: B 135 MET cc_start: 0.6224 (mmm) cc_final: 0.5870 (mmt) REVERT: B 174 MET cc_start: 0.7992 (mmm) cc_final: 0.7720 (mmm) REVERT: B 189 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7303 (pt) REVERT: C 46 LYS cc_start: 0.8404 (mmmm) cc_final: 0.7559 (mtpt) REVERT: C 77 ASP cc_start: 0.7458 (t70) cc_final: 0.6895 (m-30) REVERT: C 82 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7012 (mtm-85) REVERT: C 103 MET cc_start: 0.7226 (tmm) cc_final: 0.6479 (tpp) REVERT: C 115 LYS cc_start: 0.7458 (mtmp) cc_final: 0.7036 (mttp) REVERT: C 195 LYS cc_start: 0.6789 (mmpt) cc_final: 0.6082 (pttm) REVERT: C 198 GLU cc_start: 0.6846 (tt0) cc_final: 0.6495 (tt0) REVERT: C 230 GLU cc_start: 0.7735 (tt0) cc_final: 0.7060 (tp30) REVERT: D 63 VAL cc_start: 0.7897 (t) cc_final: 0.7670 (m) REVERT: D 68 ARG cc_start: 0.8018 (tpm170) cc_final: 0.7624 (tpp-160) REVERT: D 72 ASP cc_start: 0.6605 (m-30) cc_final: 0.5435 (m-30) REVERT: D 105 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6032 (tp30) REVERT: D 145 LYS cc_start: 0.7947 (mttm) cc_final: 0.7107 (ptpt) REVERT: D 146 GLU cc_start: 0.7544 (pm20) cc_final: 0.6668 (mp0) REVERT: D 277 HIS cc_start: 0.2855 (OUTLIER) cc_final: 0.1906 (p90) REVERT: E 56 GLN cc_start: 0.5736 (tt0) cc_final: 0.5039 (mm-40) REVERT: E 74 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: E 85 GLU cc_start: 0.6434 (tp30) cc_final: 0.6107 (tt0) REVERT: E 87 TYR cc_start: 0.5397 (m-80) cc_final: 0.4630 (m-80) REVERT: E 116 ARG cc_start: 0.6378 (mmt90) cc_final: 0.5983 (mtp180) REVERT: E 117 ARG cc_start: 0.7556 (mmm160) cc_final: 0.6683 (mtt180) REVERT: E 119 CYS cc_start: 0.7846 (m) cc_final: 0.7554 (m) REVERT: E 143 ARG cc_start: 0.5235 (ttp80) cc_final: 0.4489 (mmm-85) REVERT: E 178 ARG cc_start: 0.6398 (ptt90) cc_final: 0.6015 (ttp-110) REVERT: F 40 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7796 (mm-30) REVERT: F 67 GLN cc_start: 0.8391 (mt0) cc_final: 0.7836 (mt0) REVERT: F 115 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7047 (t) REVERT: F 118 GLU cc_start: 0.7061 (tt0) cc_final: 0.6481 (mm-30) REVERT: F 120 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7086 (tppt) REVERT: F 181 CYS cc_start: 0.8270 (t) cc_final: 0.8065 (t) REVERT: F 199 GLU cc_start: 0.7286 (tt0) cc_final: 0.6075 (tp30) REVERT: G 37 ASP cc_start: 0.7511 (m-30) cc_final: 0.7307 (m-30) REVERT: G 47 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7824 (mmtt) REVERT: G 55 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7238 (mtm110) REVERT: G 98 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7143 (mm-30) REVERT: G 106 GLU cc_start: 0.6950 (tt0) cc_final: 0.6476 (tt0) REVERT: G 198 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7494 (ttm-80) REVERT: H 4 ASN cc_start: 0.5292 (t0) cc_final: 0.4897 (t0) REVERT: H 13 GLN cc_start: 0.5987 (pt0) cc_final: 0.5479 (pm20) REVERT: H 14 LYS cc_start: 0.6369 (ttpt) cc_final: 0.5804 (tttm) REVERT: H 22 ARG cc_start: 0.6875 (mtm110) cc_final: 0.6289 (ttt-90) REVERT: H 30 LYS cc_start: 0.6679 (mmtm) cc_final: 0.5514 (ptmt) REVERT: H 32 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5320 (mtp) REVERT: H 63 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6221 (mtt) REVERT: H 101 ILE cc_start: 0.5581 (OUTLIER) cc_final: 0.5213 (mt) REVERT: H 149 LYS cc_start: 0.6024 (mtmt) cc_final: 0.5106 (mmmt) REVERT: H 154 ARG cc_start: 0.7652 (mtt-85) cc_final: 0.7144 (mtm180) REVERT: H 155 GLN cc_start: 0.5575 (mt0) cc_final: 0.5210 (mm-40) REVERT: H 197 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7870 (mt0) REVERT: I 58 LYS cc_start: 0.6306 (mttt) cc_final: 0.5850 (mttm) REVERT: I 133 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6362 (tm) REVERT: I 179 LYS cc_start: 0.7017 (tptm) cc_final: 0.6582 (tptp) REVERT: J 8 TRP cc_start: 0.8224 (p-90) cc_final: 0.7964 (p-90) REVERT: J 92 ARG cc_start: 0.7038 (tmm-80) cc_final: 0.6629 (mtt180) REVERT: J 151 GLU cc_start: 0.6406 (mm-30) cc_final: 0.6184 (mm-30) REVERT: J 153 LYS cc_start: 0.6927 (ttpt) cc_final: 0.6660 (mtmm) REVERT: J 159 SER cc_start: 0.5821 (t) cc_final: 0.5558 (p) REVERT: J 163 GLU cc_start: 0.6764 (tt0) cc_final: 0.6289 (tp30) REVERT: J 191 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: K 27 GLN cc_start: 0.7587 (tp40) cc_final: 0.7124 (pt0) REVERT: K 66 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7746 (pttt) REVERT: K 79 ARG cc_start: 0.7797 (ppp-140) cc_final: 0.6839 (ttm-80) REVERT: K 96 TYR cc_start: 0.7379 (m-80) cc_final: 0.7114 (m-80) REVERT: K 103 GLU cc_start: 0.7244 (mp0) cc_final: 0.6727 (mt-10) REVERT: K 135 ILE cc_start: 0.7916 (mp) cc_final: 0.7711 (mt) REVERT: K 153 SER cc_start: 0.7833 (t) cc_final: 0.7590 (p) REVERT: L 1 MET cc_start: 0.3611 (ttp) cc_final: 0.3400 (ttp) REVERT: L 5 LYS cc_start: 0.6289 (tppt) cc_final: 0.5963 (ttpp) REVERT: L 13 GLU cc_start: 0.7583 (tt0) cc_final: 0.7318 (tm-30) REVERT: L 74 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6494 (tp30) REVERT: L 77 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.6041 (tt0) REVERT: M 45 LYS cc_start: 0.8271 (mptp) cc_final: 0.7447 (mtmm) REVERT: M 48 LYS cc_start: 0.7487 (pptt) cc_final: 0.6928 (mttp) REVERT: M 49 GLU cc_start: 0.7525 (tm-30) cc_final: 0.6497 (mt-10) REVERT: M 84 ARG cc_start: 0.7247 (mtt90) cc_final: 0.6843 (mtt90) REVERT: M 93 LEU cc_start: 0.8328 (mt) cc_final: 0.7844 (mm) REVERT: M 97 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7512 (ttt180) REVERT: M 103 GLU cc_start: 0.8254 (pt0) cc_final: 0.7988 (pt0) REVERT: M 108 ASN cc_start: 0.7530 (p0) cc_final: 0.7075 (p0) REVERT: M 121 GLN cc_start: 0.6259 (mm-40) cc_final: 0.5816 (mp10) REVERT: N 23 LYS cc_start: 0.6172 (mttt) cc_final: 0.5521 (mtmt) REVERT: N 33 ARG cc_start: 0.1896 (ptm160) cc_final: 0.1587 (ttt-90) REVERT: N 63 LYS cc_start: 0.6079 (ttmt) cc_final: 0.5646 (tptp) REVERT: O 25 TRP cc_start: 0.7700 (p90) cc_final: 0.7213 (p90) REVERT: O 38 TYR cc_start: 0.6761 (m-80) cc_final: 0.6519 (m-80) REVERT: O 78 LYS cc_start: 0.8052 (tptp) cc_final: 0.7835 (tptp) REVERT: O 99 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7613 (mmm160) REVERT: O 140 LYS cc_start: 0.7767 (tttm) cc_final: 0.7202 (ttmm) REVERT: P 50 LYS cc_start: 0.7505 (tmtm) cc_final: 0.6573 (ttmt) REVERT: P 51 GLU cc_start: 0.7793 (tp30) cc_final: 0.7521 (tp30) REVERT: P 63 LYS cc_start: 0.5485 (mmpt) cc_final: 0.5262 (mmmt) REVERT: P 128 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6906 (mmt-90) REVERT: P 135 ILE cc_start: 0.8355 (mt) cc_final: 0.8109 (mm) REVERT: Q 15 PHE cc_start: 0.5579 (p90) cc_final: 0.5153 (p90) REVERT: Q 31 GLU cc_start: 0.6189 (mt-10) cc_final: 0.5665 (tt0) REVERT: Q 41 GLN cc_start: 0.7775 (mp10) cc_final: 0.7372 (mp10) REVERT: Q 58 LYS cc_start: 0.6330 (mmtt) cc_final: 0.5679 (mptt) REVERT: Q 62 LYS cc_start: 0.5924 (mtpm) cc_final: 0.5060 (mmtp) REVERT: Q 72 LYS cc_start: 0.6936 (mttt) cc_final: 0.6074 (ptmt) REVERT: Q 93 MET cc_start: 0.6827 (tpp) cc_final: 0.6348 (mtp) REVERT: Q 108 LYS cc_start: 0.7005 (ptpt) cc_final: 0.6565 (mmtm) REVERT: Q 118 GLU cc_start: 0.7070 (tt0) cc_final: 0.6668 (mt-10) REVERT: R 11 GLN cc_start: 0.5770 (mt0) cc_final: 0.5336 (mt0) REVERT: R 98 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7362 (tppt) REVERT: R 106 LYS cc_start: 0.6981 (ttpm) cc_final: 0.6435 (tttm) REVERT: R 110 ASP cc_start: 0.7468 (m-30) cc_final: 0.7069 (m-30) REVERT: R 146 ARG cc_start: 0.5564 (mpt90) cc_final: 0.4643 (mtm110) REVERT: S 11 LYS cc_start: 0.7783 (mttt) cc_final: 0.7365 (mmtt) REVERT: S 63 ARG cc_start: 0.5745 (mmp80) cc_final: 0.5316 (tpm170) REVERT: S 93 GLN cc_start: 0.6180 (mt0) cc_final: 0.5464 (tp40) REVERT: S 105 MET cc_start: 0.5574 (ptm) cc_final: 0.5275 (tmm) REVERT: S 107 LYS cc_start: 0.5513 (tmmt) cc_final: 0.5056 (ttmm) REVERT: S 118 GLN cc_start: 0.6690 (tt0) cc_final: 0.5664 (mm-40) REVERT: S 130 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7404 (p) REVERT: T 46 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6356 (tpt90) REVERT: T 54 LYS cc_start: 0.7075 (mttt) cc_final: 0.6708 (mtpt) REVERT: T 63 GLU cc_start: 0.7309 (mp0) cc_final: 0.6921 (mp0) REVERT: T 94 LYS cc_start: 0.6267 (mttp) cc_final: 0.5990 (mmmt) REVERT: T 126 PHE cc_start: 0.6848 (t80) cc_final: 0.6596 (t80) REVERT: U 8 ASP cc_start: 0.6941 (t70) cc_final: 0.6601 (m-30) REVERT: U 110 LEU cc_start: 0.7562 (tp) cc_final: 0.7326 (tp) REVERT: U 126 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: U 130 ASP cc_start: 0.6833 (m-30) cc_final: 0.6319 (m-30) REVERT: U 133 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6762 (mtm-85) REVERT: V 20 ILE cc_start: 0.7240 (tt) cc_final: 0.6484 (mt) REVERT: V 21 ARG cc_start: 0.6061 (ttt90) cc_final: 0.5405 (mmt-90) REVERT: V 30 LYS cc_start: 0.7261 (ptmt) cc_final: 0.6926 (mmmt) REVERT: V 44 LYS cc_start: 0.6560 (mptm) cc_final: 0.6013 (ptpt) REVERT: W 45 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6639 (mtm-85) REVERT: W 50 SER cc_start: 0.5845 (OUTLIER) cc_final: 0.5227 (p) REVERT: X 13 SER cc_start: 0.8661 (t) cc_final: 0.8288 (m) REVERT: X 41 MET cc_start: 0.8317 (mtm) cc_final: 0.8110 (mtp) REVERT: X 87 GLU cc_start: 0.8255 (tp30) cc_final: 0.7638 (mm-30) REVERT: X 115 GLU cc_start: 0.8526 (tt0) cc_final: 0.7691 (tp30) REVERT: Y 7 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8345 (tt) REVERT: Y 11 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7186 (ttp-110) REVERT: Y 37 LYS cc_start: 0.7561 (tptt) cc_final: 0.7057 (tmtt) REVERT: Y 95 GLU cc_start: 0.7925 (tt0) cc_final: 0.7530 (tt0) REVERT: Z 8 ARG cc_start: 0.7259 (mtt-85) cc_final: 0.5962 (ttt90) REVERT: Z 16 ARG cc_start: 0.7387 (mmp-170) cc_final: 0.7170 (mmt180) REVERT: Z 22 GLN cc_start: 0.8590 (pt0) cc_final: 0.8106 (pt0) REVERT: Z 39 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6743 (mp0) REVERT: Z 42 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7107 (pt0) REVERT: Z 48 TYR cc_start: 0.6018 (m-80) cc_final: 0.5633 (m-80) REVERT: Z 102 THR cc_start: 0.6020 (p) cc_final: 0.5641 (p) REVERT: Z 106 GLN cc_start: 0.7805 (mt0) cc_final: 0.7314 (mm110) REVERT: a 51 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6264 (t0) REVERT: a 60 LYS cc_start: 0.7131 (mmtt) cc_final: 0.6843 (mttt) REVERT: a 61 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6336 (mm-30) REVERT: a 92 LEU cc_start: 0.8091 (tp) cc_final: 0.7819 (tp) REVERT: b 44 ILE cc_start: 0.5667 (OUTLIER) cc_final: 0.5466 (pp) REVERT: b 89 ARG cc_start: 0.6881 (mtp-110) cc_final: 0.6401 (mtt180) REVERT: b 93 LYS cc_start: 0.7860 (mttt) cc_final: 0.7577 (mtpt) REVERT: b 94 ASP cc_start: 0.7109 (m-30) cc_final: 0.6869 (m-30) REVERT: c 26 GLN cc_start: 0.6892 (tt0) cc_final: 0.6479 (mt0) REVERT: c 36 LYS cc_start: 0.5506 (pttm) cc_final: 0.5115 (tptp) REVERT: c 72 ARG cc_start: 0.6268 (mtm180) cc_final: 0.5976 (ttm170) REVERT: d 13 ARG cc_start: 0.7128 (ttm170) cc_final: 0.6425 (mtt180) REVERT: d 33 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7892 (mt-10) REVERT: e 8 TRP cc_start: 0.8065 (t-100) cc_final: 0.7384 (t-100) REVERT: e 13 LYS cc_start: 0.7941 (mttt) cc_final: 0.7000 (mmtm) REVERT: e 38 MET cc_start: 0.7643 (ttm) cc_final: 0.7301 (ttm) REVERT: e 48 LYS cc_start: 0.7676 (tppp) cc_final: 0.7246 (ttpp) REVERT: f 96 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7714 (mm-30) REVERT: f 126 LYS cc_start: 0.6448 (mtmt) cc_final: 0.6152 (pttt) REVERT: g 95 ARG cc_start: 0.5958 (mmm160) cc_final: 0.5015 (mpt180) REVERT: h 8 ARG cc_start: 0.5080 (ttt-90) cc_final: 0.4186 (tpt90) REVERT: h 15 ASN cc_start: 0.6937 (m-40) cc_final: 0.6457 (m-40) REVERT: h 113 PHE cc_start: 0.5085 (OUTLIER) cc_final: 0.3349 (t80) REVERT: h 120 ILE cc_start: 0.6890 (mm) cc_final: 0.6434 (pt) REVERT: h 143 GLN cc_start: 0.6216 (OUTLIER) cc_final: 0.5473 (mt0) REVERT: h 217 MET cc_start: 0.5002 (mtt) cc_final: 0.4495 (ttm) REVERT: h 246 TYR cc_start: 0.6679 (t80) cc_final: 0.6286 (t80) REVERT: h 249 CYS cc_start: 0.6647 (m) cc_final: 0.6336 (m) REVERT: h 264 LYS cc_start: 0.6175 (mptt) cc_final: 0.5651 (ttpt) REVERT: h 268 ASP cc_start: 0.3837 (OUTLIER) cc_final: 0.3575 (p0) REVERT: h 305 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6567 (m-40) REVERT: n 1 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.6018 (tmm) REVERT: n 10 MET cc_start: 0.8059 (tpt) cc_final: 0.7123 (mtm) REVERT: n 21 ARG cc_start: 0.6820 (ttt90) cc_final: 0.6390 (mtp180) outliers start: 244 outliers final: 143 residues processed: 1093 average time/residue: 0.8291 time to fit residues: 1484.9714 Evaluate side-chains 1052 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 884 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 277 HIS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain S residue 43 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 126 GLN Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 41 ARG Chi-restraints excluded: chain V residue 50 VAL Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 84 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 24 GLN Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain b residue 44 ILE Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain h residue 104 HIS Chi-restraints excluded: chain h residue 113 PHE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 143 GLN Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 305 ASN Chi-restraints excluded: chain n residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 0.8980 chunk 362 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 475 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 544 optimal weight: 1.9990 chunk 440 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 325 optimal weight: 9.9990 chunk 572 optimal weight: 0.7980 chunk 160 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 91 HIS J 84 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN P 32 HIS Q 104 GLN X 15 ASN Z 63 HIS h 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 84823 Z= 0.169 Angle : 0.573 14.979 123619 Z= 0.292 Chirality : 0.036 0.307 15363 Planarity : 0.004 0.063 8630 Dihedral : 23.846 179.817 35082 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 5.53 % Allowed : 18.58 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.12), residues: 4788 helix: 0.55 (0.13), residues: 1564 sheet: -1.30 (0.17), residues: 848 loop : -1.35 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP h 177 HIS 0.006 0.001 HIS Q 79 PHE 0.026 0.002 PHE J 197 TYR 0.013 0.001 TYR L 82 ARG 0.007 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 921 time to evaluate : 4.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 ASP cc_start: 0.8363 (m-30) cc_final: 0.7500 (p0) REVERT: B 52 LYS cc_start: 0.7500 (tttt) cc_final: 0.6371 (mttp) REVERT: B 73 ASP cc_start: 0.6726 (p0) cc_final: 0.6464 (p0) REVERT: B 117 ARG cc_start: 0.7087 (mmt90) cc_final: 0.6490 (mmm160) REVERT: B 135 MET cc_start: 0.6123 (mmm) cc_final: 0.5745 (mmt) REVERT: B 174 MET cc_start: 0.7993 (mmm) cc_final: 0.7603 (mmm) REVERT: B 189 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7366 (pt) REVERT: C 46 LYS cc_start: 0.8379 (mmmm) cc_final: 0.7755 (mtmt) REVERT: C 82 ARG cc_start: 0.7856 (ttm110) cc_final: 0.7534 (mtm-85) REVERT: C 115 LYS cc_start: 0.7587 (mtmp) cc_final: 0.7168 (mttp) REVERT: C 195 LYS cc_start: 0.6781 (mmpt) cc_final: 0.6117 (pttm) REVERT: C 209 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7439 (t70) REVERT: C 210 VAL cc_start: 0.8500 (t) cc_final: 0.8229 (m) REVERT: C 230 GLU cc_start: 0.7723 (tt0) cc_final: 0.7056 (tp30) REVERT: D 68 ARG cc_start: 0.7984 (tpm170) cc_final: 0.7595 (tpp-160) REVERT: D 72 ASP cc_start: 0.6710 (m-30) cc_final: 0.5622 (m-30) REVERT: D 80 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: D 105 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6346 (tp30) REVERT: D 145 LYS cc_start: 0.7922 (mttm) cc_final: 0.7088 (ptpt) REVERT: D 146 GLU cc_start: 0.7505 (pm20) cc_final: 0.6637 (mp0) REVERT: D 277 HIS cc_start: 0.2799 (OUTLIER) cc_final: 0.1673 (p90) REVERT: E 56 GLN cc_start: 0.5746 (tt0) cc_final: 0.5101 (mm-40) REVERT: E 74 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6198 (tm-30) REVERT: E 85 GLU cc_start: 0.6399 (tp30) cc_final: 0.5967 (tt0) REVERT: E 87 TYR cc_start: 0.5539 (m-80) cc_final: 0.4709 (m-80) REVERT: E 116 ARG cc_start: 0.6388 (mmt90) cc_final: 0.5825 (mtp180) REVERT: E 117 ARG cc_start: 0.7502 (mmm160) cc_final: 0.6787 (mtt-85) REVERT: E 119 CYS cc_start: 0.7846 (m) cc_final: 0.7552 (m) REVERT: E 143 ARG cc_start: 0.4934 (ttp80) cc_final: 0.4183 (mmm-85) REVERT: E 178 ARG cc_start: 0.6280 (ptt90) cc_final: 0.6005 (ttp-110) REVERT: F 19 MET cc_start: 0.8692 (mtt) cc_final: 0.8480 (mtt) REVERT: F 40 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7788 (mm-30) REVERT: F 67 GLN cc_start: 0.8460 (mt0) cc_final: 0.7911 (mt0) REVERT: F 115 THR cc_start: 0.7200 (OUTLIER) cc_final: 0.6786 (t) REVERT: F 118 GLU cc_start: 0.7010 (tt0) cc_final: 0.6448 (mm-30) REVERT: F 120 LYS cc_start: 0.7471 (ttmp) cc_final: 0.7039 (tppt) REVERT: F 182 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7910 (ttp) REVERT: F 199 GLU cc_start: 0.7319 (tt0) cc_final: 0.6045 (tp30) REVERT: F 247 THR cc_start: 0.7209 (p) cc_final: 0.7007 (p) REVERT: G 47 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7823 (mmtt) REVERT: G 55 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7335 (mtm110) REVERT: G 76 MET cc_start: 0.8228 (mmm) cc_final: 0.7285 (tpp) REVERT: G 98 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7057 (mm-30) REVERT: G 106 GLU cc_start: 0.6933 (tt0) cc_final: 0.6464 (tt0) REVERT: G 198 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7468 (ttm-80) REVERT: H 4 ASN cc_start: 0.5302 (t0) cc_final: 0.4938 (t0) REVERT: H 13 GLN cc_start: 0.5836 (pt0) cc_final: 0.5459 (pm20) REVERT: H 14 LYS cc_start: 0.6355 (ttpt) cc_final: 0.5781 (tttm) REVERT: H 22 ARG cc_start: 0.6936 (mtm110) cc_final: 0.6344 (ttt-90) REVERT: H 30 LYS cc_start: 0.6735 (mmtm) cc_final: 0.5517 (ptmt) REVERT: H 32 MET cc_start: 0.5799 (OUTLIER) cc_final: 0.5103 (mtt) REVERT: H 57 ASP cc_start: 0.6694 (t70) cc_final: 0.6467 (t70) REVERT: H 59 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7581 (mp10) REVERT: H 63 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6193 (mtt) REVERT: H 149 LYS cc_start: 0.6019 (mtmt) cc_final: 0.5171 (mmmt) REVERT: H 154 ARG cc_start: 0.7699 (mtt-85) cc_final: 0.7128 (mtm180) REVERT: H 155 GLN cc_start: 0.5499 (mt0) cc_final: 0.5183 (mm-40) REVERT: H 197 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7942 (mt0) REVERT: I 58 LYS cc_start: 0.6396 (mttt) cc_final: 0.5990 (mttm) REVERT: I 172 THR cc_start: 0.6275 (OUTLIER) cc_final: 0.5994 (p) REVERT: I 173 PHE cc_start: 0.5377 (m-10) cc_final: 0.5134 (m-10) REVERT: I 179 LYS cc_start: 0.6957 (tptm) cc_final: 0.6603 (tptp) REVERT: J 92 ARG cc_start: 0.7040 (tmm-80) cc_final: 0.6635 (mtt180) REVERT: J 151 GLU cc_start: 0.6527 (mm-30) cc_final: 0.6309 (mm-30) REVERT: J 153 LYS cc_start: 0.6886 (ttpt) cc_final: 0.6637 (mtmm) REVERT: J 160 SER cc_start: 0.6651 (t) cc_final: 0.6384 (p) REVERT: J 163 GLU cc_start: 0.6660 (tt0) cc_final: 0.6149 (tp30) REVERT: J 191 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6849 (mt-10) REVERT: K 27 GLN cc_start: 0.7577 (tp40) cc_final: 0.7119 (pt0) REVERT: K 66 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7710 (pttt) REVERT: K 79 ARG cc_start: 0.7741 (ppp-140) cc_final: 0.6632 (ttm-80) REVERT: K 94 LEU cc_start: 0.7267 (pt) cc_final: 0.6706 (tp) REVERT: K 96 TYR cc_start: 0.7272 (m-80) cc_final: 0.7019 (m-80) REVERT: K 103 GLU cc_start: 0.7216 (mp0) cc_final: 0.6660 (mt-10) REVERT: K 135 ILE cc_start: 0.7914 (mp) cc_final: 0.7699 (mt) REVERT: L 5 LYS cc_start: 0.6429 (tppt) cc_final: 0.6055 (ttpp) REVERT: L 13 GLU cc_start: 0.7573 (tt0) cc_final: 0.7323 (tm-30) REVERT: L 31 LYS cc_start: 0.7487 (mmtt) cc_final: 0.7149 (mtmt) REVERT: L 74 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6460 (tp30) REVERT: M 45 LYS cc_start: 0.8267 (mptp) cc_final: 0.7400 (mtmm) REVERT: M 48 LYS cc_start: 0.7500 (pptt) cc_final: 0.6945 (mttp) REVERT: M 49 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6465 (mt-10) REVERT: M 84 ARG cc_start: 0.7150 (mtt90) cc_final: 0.6737 (mtt90) REVERT: M 93 LEU cc_start: 0.8322 (mt) cc_final: 0.7864 (mm) REVERT: M 103 GLU cc_start: 0.8158 (pt0) cc_final: 0.7554 (pt0) REVERT: M 108 ASN cc_start: 0.7317 (p0) cc_final: 0.6848 (p0) REVERT: M 121 GLN cc_start: 0.6258 (mm-40) cc_final: 0.5826 (mp10) REVERT: N 23 LYS cc_start: 0.6204 (mttt) cc_final: 0.5433 (mtmt) REVERT: N 33 ARG cc_start: 0.2055 (ptm160) cc_final: 0.1634 (ttt-90) REVERT: N 43 ASP cc_start: 0.5355 (OUTLIER) cc_final: 0.5084 (t70) REVERT: N 63 LYS cc_start: 0.6185 (ttmt) cc_final: 0.5949 (mttt) REVERT: O 19 ARG cc_start: 0.6526 (mtm180) cc_final: 0.6160 (ttm170) REVERT: O 25 TRP cc_start: 0.7726 (p90) cc_final: 0.7241 (p90) REVERT: O 38 TYR cc_start: 0.6738 (m-80) cc_final: 0.6486 (m-80) REVERT: O 78 LYS cc_start: 0.8031 (tptp) cc_final: 0.7827 (tptp) REVERT: O 99 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7595 (mmm160) REVERT: O 140 LYS cc_start: 0.7776 (tttm) cc_final: 0.7223 (ttmm) REVERT: P 51 GLU cc_start: 0.7773 (tp30) cc_final: 0.7478 (tp30) REVERT: P 63 LYS cc_start: 0.5477 (mmpt) cc_final: 0.5255 (mmmt) REVERT: P 128 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6990 (mmt-90) REVERT: P 135 ILE cc_start: 0.8393 (mt) cc_final: 0.8143 (mm) REVERT: Q 15 PHE cc_start: 0.5635 (p90) cc_final: 0.5122 (p90) REVERT: Q 22 LEU cc_start: 0.7417 (tp) cc_final: 0.6924 (mm) REVERT: Q 31 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5667 (tt0) REVERT: Q 41 GLN cc_start: 0.7777 (mp10) cc_final: 0.7368 (mp10) REVERT: Q 72 LYS cc_start: 0.7024 (mttt) cc_final: 0.6134 (ptmt) REVERT: Q 93 MET cc_start: 0.6759 (tpp) cc_final: 0.6479 (mmm) REVERT: Q 104 GLN cc_start: 0.6863 (tm130) cc_final: 0.6159 (tm-30) REVERT: Q 118 GLU cc_start: 0.7095 (tt0) cc_final: 0.6682 (mt-10) REVERT: R 98 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7258 (tppt) REVERT: R 106 LYS cc_start: 0.6909 (ttpm) cc_final: 0.6528 (tttm) REVERT: R 146 ARG cc_start: 0.5640 (mpt90) cc_final: 0.4827 (mtm110) REVERT: S 11 LYS cc_start: 0.7802 (mttt) cc_final: 0.7363 (mmtt) REVERT: S 37 GLU cc_start: 0.6507 (mm-30) cc_final: 0.6250 (mm-30) REVERT: S 63 ARG cc_start: 0.5700 (mmp80) cc_final: 0.5285 (tpm170) REVERT: S 93 GLN cc_start: 0.6146 (mt0) cc_final: 0.5462 (tp40) REVERT: S 105 MET cc_start: 0.5579 (ptm) cc_final: 0.5337 (tmm) REVERT: S 107 LYS cc_start: 0.5689 (tmmt) cc_final: 0.5232 (ttmm) REVERT: S 118 GLN cc_start: 0.6556 (tt0) cc_final: 0.5843 (tm-30) REVERT: S 130 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7431 (p) REVERT: T 7 GLU cc_start: 0.6070 (mp0) cc_final: 0.5429 (pm20) REVERT: T 46 ARG cc_start: 0.7342 (mmt180) cc_final: 0.6481 (tpt-90) REVERT: T 54 LYS cc_start: 0.6880 (mttt) cc_final: 0.6551 (mtpt) REVERT: T 63 GLU cc_start: 0.7255 (mp0) cc_final: 0.6871 (mp0) REVERT: T 94 LYS cc_start: 0.6256 (mttp) cc_final: 0.6020 (mmmt) REVERT: T 126 PHE cc_start: 0.6965 (t80) cc_final: 0.6680 (t80) REVERT: U 8 ASP cc_start: 0.6871 (t70) cc_final: 0.6546 (m-30) REVERT: U 108 GLU cc_start: 0.7599 (tt0) cc_final: 0.7006 (mt-10) REVERT: U 115 LYS cc_start: 0.6274 (mmtp) cc_final: 0.5960 (mmtp) REVERT: U 133 ARG cc_start: 0.7324 (mtp180) cc_final: 0.6862 (mtm-85) REVERT: V 20 ILE cc_start: 0.7263 (tt) cc_final: 0.6458 (mt) REVERT: V 21 ARG cc_start: 0.6017 (ttt90) cc_final: 0.5374 (mmt-90) REVERT: V 30 LYS cc_start: 0.7245 (ptmt) cc_final: 0.6715 (mmmt) REVERT: V 44 LYS cc_start: 0.6543 (mptm) cc_final: 0.6077 (mtpt) REVERT: V 78 ASP cc_start: 0.8811 (m-30) cc_final: 0.8522 (m-30) REVERT: W 45 ARG cc_start: 0.7048 (mtt180) cc_final: 0.6657 (mtm-85) REVERT: X 13 SER cc_start: 0.8637 (t) cc_final: 0.8263 (m) REVERT: X 41 MET cc_start: 0.8379 (mtm) cc_final: 0.8133 (mtp) REVERT: X 49 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7697 (mt-10) REVERT: X 87 GLU cc_start: 0.8303 (tp30) cc_final: 0.7647 (mm-30) REVERT: X 115 GLU cc_start: 0.8535 (tt0) cc_final: 0.7783 (tp30) REVERT: Y 11 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7131 (ttp-110) REVERT: Y 37 LYS cc_start: 0.7207 (tptt) cc_final: 0.6724 (tmtt) REVERT: Y 95 GLU cc_start: 0.7883 (tt0) cc_final: 0.7512 (tt0) REVERT: Y 114 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: Y 140 ARG cc_start: 0.5850 (mtp-110) cc_final: 0.4991 (mtp180) REVERT: Z 8 ARG cc_start: 0.7257 (mtt-85) cc_final: 0.5956 (ttt90) REVERT: Z 16 ARG cc_start: 0.7412 (mmp-170) cc_final: 0.7177 (mmt180) REVERT: Z 39 GLU cc_start: 0.7708 (mt-10) cc_final: 0.6712 (mp0) REVERT: Z 42 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7084 (pt0) REVERT: Z 48 TYR cc_start: 0.6585 (m-80) cc_final: 0.6155 (m-80) REVERT: Z 102 THR cc_start: 0.6083 (p) cc_final: 0.5840 (p) REVERT: Z 106 GLN cc_start: 0.7741 (mt0) cc_final: 0.7262 (mm110) REVERT: a 51 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6230 (t0) REVERT: a 55 TYR cc_start: 0.5876 (t80) cc_final: 0.5538 (t80) REVERT: a 60 LYS cc_start: 0.7090 (mmtt) cc_final: 0.6821 (mttt) REVERT: a 92 LEU cc_start: 0.8074 (tp) cc_final: 0.7798 (tp) REVERT: b 89 ARG cc_start: 0.6834 (mtp-110) cc_final: 0.6382 (mtt180) REVERT: b 93 LYS cc_start: 0.7861 (mttt) cc_final: 0.7581 (mtpt) REVERT: b 94 ASP cc_start: 0.7068 (m-30) cc_final: 0.6827 (m-30) REVERT: c 26 GLN cc_start: 0.6891 (tt0) cc_final: 0.6541 (mt0) REVERT: c 36 LYS cc_start: 0.5429 (pttm) cc_final: 0.5076 (tptp) REVERT: c 72 ARG cc_start: 0.6141 (mtm180) cc_final: 0.5873 (ttm170) REVERT: d 13 ARG cc_start: 0.7169 (ttm170) cc_final: 0.6515 (mtt180) REVERT: d 35 MET cc_start: 0.5960 (mmm) cc_final: 0.5732 (mmm) REVERT: d 60 GLU cc_start: 0.7673 (pm20) cc_final: 0.7408 (pm20) REVERT: e 8 TRP cc_start: 0.7906 (t-100) cc_final: 0.7285 (t-100) REVERT: e 13 LYS cc_start: 0.7934 (mttt) cc_final: 0.6985 (mmtm) REVERT: e 38 MET cc_start: 0.7551 (ttm) cc_final: 0.7189 (ttm) REVERT: e 48 LYS cc_start: 0.7662 (tppp) cc_final: 0.7222 (ttpp) REVERT: f 96 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7736 (mm-30) REVERT: f 109 MET cc_start: 0.7926 (ttp) cc_final: 0.7720 (tmm) REVERT: f 126 LYS cc_start: 0.6450 (mtmt) cc_final: 0.6077 (pttt) REVERT: g 95 ARG cc_start: 0.5937 (mmm160) cc_final: 0.5132 (mpt180) REVERT: g 132 MET cc_start: 0.4366 (ttm) cc_final: 0.4137 (ttm) REVERT: h 8 ARG cc_start: 0.5055 (ttt-90) cc_final: 0.4149 (tpt90) REVERT: h 15 ASN cc_start: 0.6861 (m-40) cc_final: 0.6369 (m-40) REVERT: h 57 ARG cc_start: 0.7186 (tpp80) cc_final: 0.6660 (mmm-85) REVERT: h 113 PHE cc_start: 0.5025 (OUTLIER) cc_final: 0.3416 (t80) REVERT: h 120 ILE cc_start: 0.6870 (mm) cc_final: 0.6397 (pt) REVERT: h 143 GLN cc_start: 0.6210 (OUTLIER) cc_final: 0.5568 (mt0) REVERT: h 177 TRP cc_start: 0.6426 (m100) cc_final: 0.5781 (m100) REVERT: h 217 MET cc_start: 0.5050 (mtt) cc_final: 0.4508 (ttm) REVERT: h 246 TYR cc_start: 0.6775 (t80) cc_final: 0.6282 (t80) REVERT: h 249 CYS cc_start: 0.6447 (m) cc_final: 0.6128 (m) REVERT: h 264 LYS cc_start: 0.6248 (mptt) cc_final: 0.5687 (ttpt) REVERT: h 268 ASP cc_start: 0.3863 (OUTLIER) cc_final: 0.3316 (p0) REVERT: h 269 GLU cc_start: 0.6253 (tt0) cc_final: 0.5922 (tp30) REVERT: h 305 ASN cc_start: 0.6970 (OUTLIER) cc_final: 0.6529 (m-40) REVERT: n 1 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.6273 (tmm) REVERT: n 21 ARG cc_start: 0.6844 (ttt90) cc_final: 0.6327 (mtp180) outliers start: 232 outliers final: 147 residues processed: 1070 average time/residue: 0.8320 time to fit residues: 1465.5813 Evaluate side-chains 1043 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 873 time to evaluate : 4.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 277 HIS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 43 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 41 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 84 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 114 ASP Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 104 HIS Chi-restraints excluded: chain h residue 113 PHE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 143 GLN Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 305 ASN Chi-restraints excluded: chain n residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 0.0570 chunk 574 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 374 optimal weight: 0.5980 chunk 157 optimal weight: 10.0000 chunk 638 optimal weight: 4.9990 chunk 530 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 335 optimal weight: 6.9990 overall best weight: 3.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN C 202 GLN D 178 HIS E 159 HIS ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN J 52 ASN J 167 GLN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN P 32 HIS Q 128 HIS ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 24 GLN Z 63 HIS h 143 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 84823 Z= 0.328 Angle : 0.689 14.508 123619 Z= 0.348 Chirality : 0.042 0.322 15363 Planarity : 0.005 0.062 8630 Dihedral : 23.973 179.870 35080 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 6.44 % Allowed : 19.25 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.12), residues: 4788 helix: 0.27 (0.13), residues: 1548 sheet: -1.36 (0.17), residues: 862 loop : -1.45 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP h 17 HIS 0.009 0.001 HIS h 188 PHE 0.029 0.002 PHE D 269 TYR 0.018 0.002 TYR E 107 ARG 0.010 0.001 ARG O 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 861 time to evaluate : 4.558 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: B 52 LYS cc_start: 0.7383 (tttt) cc_final: 0.6257 (mttp) REVERT: B 94 THR cc_start: 0.8222 (OUTLIER) cc_final: 0.7884 (p) REVERT: B 117 ARG cc_start: 0.7277 (mmt90) cc_final: 0.6589 (mmm160) REVERT: B 135 MET cc_start: 0.6127 (mmm) cc_final: 0.5776 (mmt) REVERT: B 174 MET cc_start: 0.8257 (mmm) cc_final: 0.7942 (mmm) REVERT: B 189 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7382 (pt) REVERT: C 46 LYS cc_start: 0.8670 (mmmm) cc_final: 0.7767 (mtmt) REVERT: C 77 ASP cc_start: 0.7625 (t0) cc_final: 0.7255 (m-30) REVERT: C 82 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7234 (mtp85) REVERT: C 103 MET cc_start: 0.7831 (tmm) cc_final: 0.6925 (tpp) REVERT: C 115 LYS cc_start: 0.7547 (mtmp) cc_final: 0.7191 (mttp) REVERT: C 195 LYS cc_start: 0.6784 (mmpt) cc_final: 0.6087 (pttm) REVERT: C 198 GLU cc_start: 0.6863 (tt0) cc_final: 0.6495 (tt0) REVERT: D 68 ARG cc_start: 0.8048 (tpm170) cc_final: 0.7615 (tpp-160) REVERT: D 72 ASP cc_start: 0.6408 (m-30) cc_final: 0.5335 (m-30) REVERT: D 80 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: D 82 TYR cc_start: 0.8423 (m-10) cc_final: 0.8065 (m-80) REVERT: D 105 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6247 (tp30) REVERT: D 145 LYS cc_start: 0.7965 (mttm) cc_final: 0.7095 (ptpt) REVERT: D 146 GLU cc_start: 0.7417 (pm20) cc_final: 0.6700 (mp0) REVERT: D 277 HIS cc_start: 0.3075 (OUTLIER) cc_final: 0.1700 (p90) REVERT: E 56 GLN cc_start: 0.5652 (tt0) cc_final: 0.5129 (mm-40) REVERT: E 74 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: E 89 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5252 (tt0) REVERT: E 116 ARG cc_start: 0.6463 (mmt90) cc_final: 0.5892 (mtp180) REVERT: E 117 ARG cc_start: 0.7653 (mmm160) cc_final: 0.6875 (mtt90) REVERT: E 119 CYS cc_start: 0.7904 (m) cc_final: 0.7638 (m) REVERT: E 143 ARG cc_start: 0.5053 (ttp80) cc_final: 0.4388 (mmm-85) REVERT: E 207 HIS cc_start: 0.7040 (OUTLIER) cc_final: 0.6827 (t70) REVERT: F 19 MET cc_start: 0.8829 (mtt) cc_final: 0.8586 (mtt) REVERT: F 40 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7701 (mm-30) REVERT: F 67 GLN cc_start: 0.8242 (mt0) cc_final: 0.7715 (mt0) REVERT: F 118 GLU cc_start: 0.7069 (tt0) cc_final: 0.6561 (mm-30) REVERT: F 120 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6791 (tppt) REVERT: F 182 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7954 (tpp) REVERT: F 199 GLU cc_start: 0.7302 (tt0) cc_final: 0.6011 (tp30) REVERT: F 250 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6856 (mt-10) REVERT: G 36 GLN cc_start: 0.7454 (tp40) cc_final: 0.7173 (tp40) REVERT: G 47 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7871 (mmtt) REVERT: G 55 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7322 (mtm110) REVERT: G 106 GLU cc_start: 0.6972 (tt0) cc_final: 0.6499 (tt0) REVERT: G 172 CYS cc_start: 0.7570 (m) cc_final: 0.7297 (m) REVERT: G 198 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7468 (ttm-80) REVERT: H 22 ARG cc_start: 0.6945 (mtm110) cc_final: 0.6297 (ttt-90) REVERT: H 30 LYS cc_start: 0.6789 (mmtm) cc_final: 0.5916 (mmtt) REVERT: H 32 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5517 (mtp) REVERT: H 59 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7615 (mp10) REVERT: H 63 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6700 (mtt) REVERT: H 149 LYS cc_start: 0.5819 (mtmt) cc_final: 0.4903 (mmmt) REVERT: H 154 ARG cc_start: 0.7684 (mtt-85) cc_final: 0.7124 (mtm180) REVERT: H 155 GLN cc_start: 0.5375 (mt0) cc_final: 0.5044 (mm-40) REVERT: H 197 GLN cc_start: 0.8343 (tp-100) cc_final: 0.7960 (mt0) REVERT: I 58 LYS cc_start: 0.6594 (mttt) cc_final: 0.6205 (mttm) REVERT: I 113 LYS cc_start: 0.3694 (OUTLIER) cc_final: 0.2022 (mmtm) REVERT: J 92 ARG cc_start: 0.7165 (tmm-80) cc_final: 0.6762 (mtt180) REVERT: J 163 GLU cc_start: 0.6949 (tt0) cc_final: 0.6291 (tp30) REVERT: J 191 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: K 27 GLN cc_start: 0.7569 (tp40) cc_final: 0.7137 (pt0) REVERT: K 66 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7854 (pttt) REVERT: K 79 ARG cc_start: 0.7680 (ppp-140) cc_final: 0.6685 (ttm-80) REVERT: K 103 GLU cc_start: 0.7297 (mp0) cc_final: 0.6863 (mt-10) REVERT: K 143 ASN cc_start: 0.7187 (t0) cc_final: 0.6835 (t0) REVERT: L 5 LYS cc_start: 0.6485 (tppt) cc_final: 0.5967 (ttpp) REVERT: L 13 GLU cc_start: 0.7667 (tt0) cc_final: 0.7420 (tm-30) REVERT: L 74 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6321 (tp30) REVERT: M 45 LYS cc_start: 0.8257 (mptp) cc_final: 0.7936 (mttp) REVERT: M 48 LYS cc_start: 0.7467 (pptt) cc_final: 0.7112 (ptmt) REVERT: M 49 GLU cc_start: 0.7550 (tm-30) cc_final: 0.6514 (mt-10) REVERT: M 93 LEU cc_start: 0.8256 (mt) cc_final: 0.7671 (mm) REVERT: M 97 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7480 (ttt180) REVERT: M 103 GLU cc_start: 0.8330 (pt0) cc_final: 0.7922 (pt0) REVERT: M 121 GLN cc_start: 0.6190 (mm-40) cc_final: 0.5762 (mp10) REVERT: N 23 LYS cc_start: 0.6169 (mttt) cc_final: 0.5463 (mtmt) REVERT: N 63 LYS cc_start: 0.6152 (ttmt) cc_final: 0.5788 (mttt) REVERT: O 20 ARG cc_start: 0.6865 (mtm-85) cc_final: 0.6484 (mtm-85) REVERT: O 25 TRP cc_start: 0.7616 (p90) cc_final: 0.7138 (p90) REVERT: O 38 TYR cc_start: 0.6843 (m-80) cc_final: 0.6636 (m-80) REVERT: O 96 VAL cc_start: 0.8092 (t) cc_final: 0.7745 (m) REVERT: O 99 ARG cc_start: 0.7883 (mtp180) cc_final: 0.7625 (mmm160) REVERT: O 110 ASP cc_start: 0.8020 (t0) cc_final: 0.7718 (t0) REVERT: O 140 LYS cc_start: 0.7794 (tttm) cc_final: 0.7248 (ttmm) REVERT: P 28 PHE cc_start: 0.7932 (m-80) cc_final: 0.7682 (m-80) REVERT: P 50 LYS cc_start: 0.7365 (tttp) cc_final: 0.7156 (tttp) REVERT: P 51 GLU cc_start: 0.7761 (tp30) cc_final: 0.7458 (tp30) REVERT: P 63 LYS cc_start: 0.5626 (mmpt) cc_final: 0.5310 (mmmt) REVERT: P 72 TYR cc_start: 0.8066 (t80) cc_final: 0.7761 (t80) REVERT: P 128 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6652 (mmt-90) REVERT: P 135 ILE cc_start: 0.8422 (mt) cc_final: 0.8169 (mm) REVERT: Q 31 GLU cc_start: 0.6162 (mt-10) cc_final: 0.5700 (tt0) REVERT: Q 41 GLN cc_start: 0.7755 (mp10) cc_final: 0.7320 (mp10) REVERT: Q 72 LYS cc_start: 0.7123 (mttt) cc_final: 0.6211 (ptmt) REVERT: Q 93 MET cc_start: 0.6593 (tpp) cc_final: 0.6227 (ttp) REVERT: Q 118 GLU cc_start: 0.7168 (tt0) cc_final: 0.6763 (mt-10) REVERT: R 98 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7289 (tppt) REVERT: R 146 ARG cc_start: 0.5606 (mpt90) cc_final: 0.4807 (mtm110) REVERT: S 11 LYS cc_start: 0.7777 (mttt) cc_final: 0.7335 (mmtt) REVERT: S 93 GLN cc_start: 0.6157 (mt0) cc_final: 0.5513 (tp40) REVERT: S 107 LYS cc_start: 0.5985 (tmmt) cc_final: 0.5492 (ttmm) REVERT: S 111 PHE cc_start: 0.5312 (OUTLIER) cc_final: 0.5062 (m-80) REVERT: S 118 GLN cc_start: 0.6279 (tt0) cc_final: 0.5267 (tm-30) REVERT: S 130 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7634 (p) REVERT: T 46 ARG cc_start: 0.7299 (mmt180) cc_final: 0.6385 (tpt-90) REVERT: T 54 LYS cc_start: 0.6961 (mttt) cc_final: 0.6615 (mtpt) REVERT: T 63 GLU cc_start: 0.7102 (mp0) cc_final: 0.6715 (mp0) REVERT: T 94 LYS cc_start: 0.6367 (mttp) cc_final: 0.5974 (mmmt) REVERT: T 126 PHE cc_start: 0.6942 (t80) cc_final: 0.6683 (t80) REVERT: T 129 LEU cc_start: 0.7287 (mt) cc_final: 0.7003 (mt) REVERT: T 136 THR cc_start: 0.5917 (p) cc_final: 0.5701 (p) REVERT: U 8 ASP cc_start: 0.7101 (t0) cc_final: 0.6695 (m-30) REVERT: U 133 ARG cc_start: 0.7224 (mtp180) cc_final: 0.6728 (mtm-85) REVERT: V 20 ILE cc_start: 0.7367 (tt) cc_final: 0.6546 (mt) REVERT: V 21 ARG cc_start: 0.6004 (ttt90) cc_final: 0.5296 (mmt-90) REVERT: V 27 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7480 (mtp-110) REVERT: V 30 LYS cc_start: 0.7292 (ptmt) cc_final: 0.6793 (mmmt) REVERT: V 44 LYS cc_start: 0.6466 (mptm) cc_final: 0.5979 (mtpt) REVERT: W 45 ARG cc_start: 0.6974 (mtt180) cc_final: 0.6701 (mtm-85) REVERT: W 50 SER cc_start: 0.5842 (OUTLIER) cc_final: 0.5088 (p) REVERT: X 13 SER cc_start: 0.8680 (t) cc_final: 0.8253 (m) REVERT: X 41 MET cc_start: 0.8578 (mtm) cc_final: 0.8184 (mtp) REVERT: X 87 GLU cc_start: 0.8286 (tp30) cc_final: 0.7829 (mm-30) REVERT: Y 11 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7674 (ttm110) REVERT: Y 37 LYS cc_start: 0.7173 (tptt) cc_final: 0.6675 (tmtt) REVERT: Y 95 GLU cc_start: 0.7953 (tt0) cc_final: 0.7609 (tt0) REVERT: Y 140 ARG cc_start: 0.5926 (mtp-110) cc_final: 0.4859 (mtp180) REVERT: Z 8 ARG cc_start: 0.7313 (mtt-85) cc_final: 0.5958 (ttt90) REVERT: Z 15 ASN cc_start: 0.7204 (t0) cc_final: 0.6909 (t0) REVERT: Z 39 GLU cc_start: 0.7731 (mt-10) cc_final: 0.6960 (mp0) REVERT: Z 42 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7105 (pt0) REVERT: Z 48 TYR cc_start: 0.6582 (m-80) cc_final: 0.6054 (m-80) REVERT: Z 102 THR cc_start: 0.6165 (p) cc_final: 0.5704 (p) REVERT: Z 106 GLN cc_start: 0.7794 (mt0) cc_final: 0.7264 (mm110) REVERT: a 51 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6376 (t0) REVERT: a 60 LYS cc_start: 0.7092 (mmtt) cc_final: 0.6871 (mttt) REVERT: a 92 LEU cc_start: 0.7857 (tp) cc_final: 0.7576 (tp) REVERT: b 73 TYR cc_start: 0.8208 (m-80) cc_final: 0.7682 (m-80) REVERT: b 89 ARG cc_start: 0.6864 (mtp-110) cc_final: 0.6323 (mtt180) REVERT: b 93 LYS cc_start: 0.7847 (mttt) cc_final: 0.7597 (mtpt) REVERT: b 94 ASP cc_start: 0.7083 (m-30) cc_final: 0.6809 (m-30) REVERT: c 26 GLN cc_start: 0.7006 (tt0) cc_final: 0.6637 (mt0) REVERT: c 36 LYS cc_start: 0.5441 (pttm) cc_final: 0.5087 (tptp) REVERT: c 72 ARG cc_start: 0.6285 (mtm180) cc_final: 0.6012 (ttm170) REVERT: d 13 ARG cc_start: 0.7110 (ttm170) cc_final: 0.6623 (ttm170) REVERT: d 35 MET cc_start: 0.6155 (mmm) cc_final: 0.5883 (mmm) REVERT: d 54 ASP cc_start: 0.7561 (p0) cc_final: 0.7282 (p0) REVERT: e 8 TRP cc_start: 0.8227 (t-100) cc_final: 0.7486 (t-100) REVERT: e 13 LYS cc_start: 0.7905 (mttt) cc_final: 0.6923 (mmtm) REVERT: e 38 MET cc_start: 0.7623 (ttm) cc_final: 0.7293 (ttm) REVERT: f 96 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7734 (mm-30) REVERT: f 109 MET cc_start: 0.7941 (ttp) cc_final: 0.7444 (ppp) REVERT: f 126 LYS cc_start: 0.6423 (mtmt) cc_final: 0.5915 (mmtt) REVERT: g 95 ARG cc_start: 0.5575 (mmm160) cc_final: 0.5311 (tpp-160) REVERT: g 132 MET cc_start: 0.4275 (ttm) cc_final: 0.4073 (ttm) REVERT: h 8 ARG cc_start: 0.5049 (ttt-90) cc_final: 0.4390 (tpt90) REVERT: h 15 ASN cc_start: 0.6908 (m-40) cc_final: 0.6484 (m-40) REVERT: h 30 MET cc_start: 0.4198 (tmm) cc_final: 0.3642 (mmt) REVERT: h 57 ARG cc_start: 0.7168 (tpp80) cc_final: 0.6618 (mmm-85) REVERT: h 89 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6779 (tt) REVERT: h 113 PHE cc_start: 0.5560 (OUTLIER) cc_final: 0.3725 (t80) REVERT: h 120 ILE cc_start: 0.6709 (OUTLIER) cc_final: 0.6308 (pt) REVERT: h 217 MET cc_start: 0.5175 (mtt) cc_final: 0.4702 (ttm) REVERT: h 246 TYR cc_start: 0.6766 (t80) cc_final: 0.6204 (t80) REVERT: h 264 LYS cc_start: 0.6463 (mptt) cc_final: 0.5698 (ttpt) REVERT: h 268 ASP cc_start: 0.4064 (OUTLIER) cc_final: 0.3697 (p0) REVERT: h 305 ASN cc_start: 0.7024 (OUTLIER) cc_final: 0.6532 (m-40) REVERT: n 1 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.6345 (tmm) REVERT: n 21 ARG cc_start: 0.6701 (ttt90) cc_final: 0.6242 (mtp180) outliers start: 270 outliers final: 181 residues processed: 1047 average time/residue: 0.8323 time to fit residues: 1435.0229 Evaluate side-chains 1037 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 830 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 277 HIS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 43 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 111 PHE Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 41 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 CYS Chi-restraints excluded: chain V residue 84 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain X residue 24 GLN Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 97 ASN Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain e residue 54 LYS Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 104 HIS Chi-restraints excluded: chain h residue 113 PHE Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 305 ASN Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 16 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 363 optimal weight: 0.8980 chunk 466 optimal weight: 2.9990 chunk 361 optimal weight: 0.9990 chunk 537 optimal weight: 4.9990 chunk 356 optimal weight: 3.9990 chunk 636 optimal weight: 5.9990 chunk 398 optimal weight: 0.9980 chunk 387 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 GLN F 188 ASN J 84 ASN J 167 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN P 32 HIS Q 104 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 HIS h 143 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 84823 Z= 0.219 Angle : 0.613 14.888 123619 Z= 0.311 Chirality : 0.038 0.315 15363 Planarity : 0.004 0.065 8630 Dihedral : 23.921 179.816 35080 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 5.82 % Allowed : 19.94 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.12), residues: 4788 helix: 0.40 (0.13), residues: 1555 sheet: -1.30 (0.17), residues: 867 loop : -1.38 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP h 17 HIS 0.006 0.001 HIS Q 79 PHE 0.031 0.002 PHE D 269 TYR 0.017 0.002 TYR L 78 ARG 0.006 0.001 ARG X 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 865 time to evaluate : 4.498 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: B 52 LYS cc_start: 0.7569 (tttt) cc_final: 0.6389 (mttp) REVERT: B 117 ARG cc_start: 0.7268 (mmt90) cc_final: 0.6577 (mmm160) REVERT: B 135 MET cc_start: 0.6138 (mmm) cc_final: 0.5790 (mmt) REVERT: B 174 MET cc_start: 0.8076 (mmm) cc_final: 0.7670 (mmm) REVERT: B 189 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7536 (pt) REVERT: C 38 MET cc_start: 0.7313 (ptp) cc_final: 0.6744 (mpp) REVERT: C 46 LYS cc_start: 0.8652 (mmmm) cc_final: 0.7562 (mtpt) REVERT: C 77 ASP cc_start: 0.7600 (t0) cc_final: 0.7253 (m-30) REVERT: C 82 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7034 (mtp85) REVERT: C 103 MET cc_start: 0.7713 (tmm) cc_final: 0.6817 (tpp) REVERT: C 115 LYS cc_start: 0.7526 (mtmp) cc_final: 0.7181 (mttp) REVERT: C 133 TYR cc_start: 0.6920 (m-80) cc_final: 0.6572 (m-80) REVERT: C 195 LYS cc_start: 0.6815 (mmpt) cc_final: 0.6160 (pttm) REVERT: C 209 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7566 (t70) REVERT: D 68 ARG cc_start: 0.7999 (tpm170) cc_final: 0.7672 (tpp-160) REVERT: D 72 ASP cc_start: 0.6590 (m-30) cc_final: 0.5593 (m-30) REVERT: D 80 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7346 (pt0) REVERT: D 82 TYR cc_start: 0.8384 (m-10) cc_final: 0.8029 (m-80) REVERT: D 92 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6111 (mt-10) REVERT: D 105 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6045 (tp30) REVERT: D 145 LYS cc_start: 0.7922 (mttm) cc_final: 0.7113 (ptpt) REVERT: D 146 GLU cc_start: 0.7393 (pm20) cc_final: 0.6684 (mp0) REVERT: E 56 GLN cc_start: 0.5613 (tt0) cc_final: 0.5164 (mm-40) REVERT: E 74 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: E 89 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: E 116 ARG cc_start: 0.6373 (mmt90) cc_final: 0.5846 (mtp180) REVERT: E 117 ARG cc_start: 0.7756 (mmm160) cc_final: 0.6967 (mtt180) REVERT: E 119 CYS cc_start: 0.7891 (m) cc_final: 0.7600 (m) REVERT: E 143 ARG cc_start: 0.4927 (ttp80) cc_final: 0.4329 (mmm-85) REVERT: E 157 MET cc_start: 0.8135 (mmm) cc_final: 0.7759 (mmm) REVERT: E 207 HIS cc_start: 0.7053 (OUTLIER) cc_final: 0.6783 (t70) REVERT: F 19 MET cc_start: 0.8655 (mtt) cc_final: 0.8425 (mtt) REVERT: F 40 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7688 (mm-30) REVERT: F 67 GLN cc_start: 0.8406 (mt0) cc_final: 0.7887 (mt0) REVERT: F 115 THR cc_start: 0.7008 (OUTLIER) cc_final: 0.6692 (t) REVERT: F 118 GLU cc_start: 0.7020 (tt0) cc_final: 0.6494 (mm-30) REVERT: F 120 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6769 (tppt) REVERT: F 182 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8003 (tpp) REVERT: F 199 GLU cc_start: 0.7333 (tt0) cc_final: 0.6010 (tp30) REVERT: F 212 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: F 250 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6790 (mt-10) REVERT: G 36 GLN cc_start: 0.7398 (tp40) cc_final: 0.7086 (tp40) REVERT: G 47 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7672 (mmtt) REVERT: G 55 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7247 (mtm110) REVERT: G 106 GLU cc_start: 0.6923 (tt0) cc_final: 0.6431 (tt0) REVERT: G 172 CYS cc_start: 0.7617 (m) cc_final: 0.7307 (m) REVERT: G 198 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7499 (ttm-80) REVERT: H 4 ASN cc_start: 0.5824 (t0) cc_final: 0.5403 (t0) REVERT: H 22 ARG cc_start: 0.6945 (mtm110) cc_final: 0.6343 (ttt-90) REVERT: H 30 LYS cc_start: 0.6886 (mmtm) cc_final: 0.6170 (mmtt) REVERT: H 32 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.5372 (mtp) REVERT: H 59 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7640 (mp10) REVERT: H 63 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6469 (mtt) REVERT: H 149 LYS cc_start: 0.5815 (mtmt) cc_final: 0.4881 (mmmt) REVERT: H 154 ARG cc_start: 0.7704 (mtt-85) cc_final: 0.7104 (mtm180) REVERT: H 155 GLN cc_start: 0.5350 (mt0) cc_final: 0.5034 (mm-40) REVERT: H 197 GLN cc_start: 0.8320 (tp-100) cc_final: 0.7950 (mt0) REVERT: I 58 LYS cc_start: 0.6575 (mttt) cc_final: 0.6190 (mttm) REVERT: I 113 LYS cc_start: 0.3649 (OUTLIER) cc_final: 0.2022 (mmtm) REVERT: J 28 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8277 (mt-10) REVERT: J 92 ARG cc_start: 0.7154 (tmm-80) cc_final: 0.6757 (mtt180) REVERT: J 157 LYS cc_start: 0.7605 (ttpt) cc_final: 0.7375 (ttpt) REVERT: J 163 GLU cc_start: 0.6927 (tt0) cc_final: 0.6211 (tp30) REVERT: J 191 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6764 (mt-10) REVERT: K 27 GLN cc_start: 0.7545 (tp40) cc_final: 0.7116 (pt0) REVERT: K 66 LYS cc_start: 0.8377 (mmtt) cc_final: 0.7872 (pttt) REVERT: K 79 ARG cc_start: 0.7650 (ppp-140) cc_final: 0.6636 (ttm-80) REVERT: K 103 GLU cc_start: 0.7336 (mp0) cc_final: 0.6859 (mt-10) REVERT: K 135 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8015 (mp) REVERT: L 5 LYS cc_start: 0.6507 (tppt) cc_final: 0.5960 (ttpp) REVERT: L 74 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6365 (tp30) REVERT: M 45 LYS cc_start: 0.8238 (mptp) cc_final: 0.7948 (mttp) REVERT: M 48 LYS cc_start: 0.7427 (pptt) cc_final: 0.7102 (ptmt) REVERT: M 49 GLU cc_start: 0.7539 (tm-30) cc_final: 0.6600 (mt-10) REVERT: M 93 LEU cc_start: 0.8325 (mt) cc_final: 0.7844 (mm) REVERT: M 97 ARG cc_start: 0.8038 (ttp-110) cc_final: 0.7438 (ttt180) REVERT: M 103 GLU cc_start: 0.8252 (pt0) cc_final: 0.7823 (pt0) REVERT: M 121 GLN cc_start: 0.6051 (mm-40) cc_final: 0.5637 (mp10) REVERT: N 23 LYS cc_start: 0.6364 (mttt) cc_final: 0.5623 (mtmt) REVERT: N 43 ASP cc_start: 0.5473 (t70) cc_final: 0.5225 (t70) REVERT: N 63 LYS cc_start: 0.6209 (ttmt) cc_final: 0.5735 (mttt) REVERT: O 38 TYR cc_start: 0.6857 (m-80) cc_final: 0.6642 (m-80) REVERT: O 99 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7622 (mmm160) REVERT: O 110 ASP cc_start: 0.7991 (t0) cc_final: 0.7685 (t0) REVERT: O 140 LYS cc_start: 0.7808 (tttm) cc_final: 0.7233 (ttmm) REVERT: P 51 GLU cc_start: 0.7684 (tp30) cc_final: 0.7380 (tp30) REVERT: P 63 LYS cc_start: 0.5597 (mmpt) cc_final: 0.5309 (mmmt) REVERT: P 135 ILE cc_start: 0.8394 (mt) cc_final: 0.8142 (mm) REVERT: Q 22 LEU cc_start: 0.7434 (tp) cc_final: 0.7117 (mm) REVERT: Q 31 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5706 (tt0) REVERT: Q 41 GLN cc_start: 0.7907 (mp10) cc_final: 0.7458 (mp10) REVERT: Q 72 LYS cc_start: 0.7115 (mttt) cc_final: 0.6214 (ptmt) REVERT: Q 118 GLU cc_start: 0.7153 (tt0) cc_final: 0.6751 (mt-10) REVERT: R 98 LYS cc_start: 0.7810 (ttmt) cc_final: 0.7229 (tppt) REVERT: R 106 LYS cc_start: 0.6910 (ttpm) cc_final: 0.6532 (tttp) REVERT: R 146 ARG cc_start: 0.5720 (mpt90) cc_final: 0.4729 (mtm110) REVERT: S 11 LYS cc_start: 0.7761 (mttt) cc_final: 0.7321 (mmtt) REVERT: S 93 GLN cc_start: 0.6121 (mt0) cc_final: 0.5512 (tp40) REVERT: S 107 LYS cc_start: 0.5957 (tmmt) cc_final: 0.5484 (ttmm) REVERT: S 118 GLN cc_start: 0.6268 (tt0) cc_final: 0.5283 (tm-30) REVERT: S 130 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7514 (p) REVERT: T 46 ARG cc_start: 0.7362 (mmt180) cc_final: 0.6371 (tpt-90) REVERT: T 54 LYS cc_start: 0.6846 (mttt) cc_final: 0.6518 (mtpt) REVERT: T 63 GLU cc_start: 0.7053 (mp0) cc_final: 0.6683 (mp0) REVERT: T 94 LYS cc_start: 0.6326 (mttp) cc_final: 0.5881 (mmmt) REVERT: T 126 PHE cc_start: 0.6937 (t80) cc_final: 0.6704 (t80) REVERT: U 8 ASP cc_start: 0.7080 (t0) cc_final: 0.6771 (m-30) REVERT: U 133 ARG cc_start: 0.7161 (mtp180) cc_final: 0.6650 (mtm-85) REVERT: V 20 ILE cc_start: 0.7273 (tt) cc_final: 0.6482 (mt) REVERT: V 21 ARG cc_start: 0.5984 (ttt90) cc_final: 0.5272 (mmt-90) REVERT: V 30 LYS cc_start: 0.7623 (ptmt) cc_final: 0.7039 (mmmt) REVERT: V 44 LYS cc_start: 0.6481 (mptm) cc_final: 0.5991 (mtpt) REVERT: W 45 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6730 (mtm-85) REVERT: W 50 SER cc_start: 0.5890 (OUTLIER) cc_final: 0.5147 (p) REVERT: X 13 SER cc_start: 0.8663 (t) cc_final: 0.8250 (m) REVERT: X 41 MET cc_start: 0.8512 (mtm) cc_final: 0.8310 (mtp) REVERT: X 87 GLU cc_start: 0.8208 (tp30) cc_final: 0.7769 (mm-30) REVERT: X 115 GLU cc_start: 0.8560 (tt0) cc_final: 0.7761 (tp30) REVERT: Y 11 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7533 (ttm110) REVERT: Y 37 LYS cc_start: 0.7175 (tptt) cc_final: 0.6675 (tmtt) REVERT: Y 95 GLU cc_start: 0.7902 (tt0) cc_final: 0.7552 (tt0) REVERT: Y 139 GLU cc_start: 0.5485 (mm-30) cc_final: 0.4372 (mm-30) REVERT: Y 140 ARG cc_start: 0.5832 (mtp-110) cc_final: 0.4811 (mtp180) REVERT: Z 8 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.6025 (ttt90) REVERT: Z 15 ASN cc_start: 0.7287 (t0) cc_final: 0.6962 (t0) REVERT: Z 39 GLU cc_start: 0.7771 (mt-10) cc_final: 0.6873 (mp0) REVERT: Z 42 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7115 (pt0) REVERT: Z 48 TYR cc_start: 0.6503 (m-80) cc_final: 0.6002 (m-80) REVERT: Z 106 GLN cc_start: 0.7770 (mt0) cc_final: 0.7275 (mm110) REVERT: a 51 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6216 (t0) REVERT: a 60 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6982 (mttt) REVERT: a 92 LEU cc_start: 0.7850 (tp) cc_final: 0.7566 (tp) REVERT: b 89 ARG cc_start: 0.6814 (mtp-110) cc_final: 0.6309 (mtt180) REVERT: b 93 LYS cc_start: 0.7841 (mttt) cc_final: 0.7585 (mtpt) REVERT: b 94 ASP cc_start: 0.6986 (m-30) cc_final: 0.6729 (m-30) REVERT: c 26 GLN cc_start: 0.6920 (tt0) cc_final: 0.6509 (mt0) REVERT: c 36 LYS cc_start: 0.5448 (pttm) cc_final: 0.5085 (tptp) REVERT: c 72 ARG cc_start: 0.6255 (mtm180) cc_final: 0.6006 (ttm170) REVERT: d 54 ASP cc_start: 0.7373 (p0) cc_final: 0.7078 (p0) REVERT: d 57 THR cc_start: 0.7833 (m) cc_final: 0.7630 (m) REVERT: e 8 TRP cc_start: 0.8237 (t-100) cc_final: 0.7543 (t-100) REVERT: e 13 LYS cc_start: 0.7837 (mttt) cc_final: 0.6897 (mmtm) REVERT: e 38 MET cc_start: 0.7536 (ttm) cc_final: 0.7205 (ttm) REVERT: e 48 LYS cc_start: 0.7687 (tppp) cc_final: 0.7178 (ttpp) REVERT: f 81 ARG cc_start: 0.7098 (mtp85) cc_final: 0.6811 (mpt180) REVERT: f 96 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7750 (mm-30) REVERT: f 109 MET cc_start: 0.7871 (ttp) cc_final: 0.7651 (tmm) REVERT: f 126 LYS cc_start: 0.6418 (mtmt) cc_final: 0.6097 (pttt) REVERT: g 132 MET cc_start: 0.4304 (ttm) cc_final: 0.4082 (ttm) REVERT: h 8 ARG cc_start: 0.5192 (ttt-90) cc_final: 0.4375 (tpt90) REVERT: h 15 ASN cc_start: 0.6844 (m-40) cc_final: 0.6403 (m-40) REVERT: h 30 MET cc_start: 0.4255 (tmm) cc_final: 0.3671 (mmt) REVERT: h 57 ARG cc_start: 0.7174 (tpp80) cc_final: 0.6610 (mmm-85) REVERT: h 89 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6861 (tt) REVERT: h 113 PHE cc_start: 0.5533 (OUTLIER) cc_final: 0.3760 (t80) REVERT: h 120 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6314 (pt) REVERT: h 177 TRP cc_start: 0.6315 (m100) cc_final: 0.5758 (m100) REVERT: h 217 MET cc_start: 0.5312 (mtt) cc_final: 0.4918 (ttm) REVERT: h 246 TYR cc_start: 0.6806 (t80) cc_final: 0.6260 (t80) REVERT: h 264 LYS cc_start: 0.6480 (mptt) cc_final: 0.5693 (ttpt) REVERT: h 268 ASP cc_start: 0.4366 (OUTLIER) cc_final: 0.3641 (p0) REVERT: h 305 ASN cc_start: 0.6914 (OUTLIER) cc_final: 0.6362 (m-40) REVERT: n 1 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.6151 (tmm) REVERT: n 21 ARG cc_start: 0.6757 (ttt90) cc_final: 0.5950 (tpt90) outliers start: 244 outliers final: 175 residues processed: 1024 average time/residue: 0.8287 time to fit residues: 1399.1969 Evaluate side-chains 1049 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 847 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 43 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 41 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 CYS Chi-restraints excluded: chain V residue 84 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain X residue 24 GLN Chi-restraints excluded: chain X residue 27 ILE Chi-restraints excluded: chain X residue 32 LYS Chi-restraints excluded: chain X residue 46 TYR Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 11 ARG Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 97 ASN Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain c residue 57 VAL Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 104 HIS Chi-restraints excluded: chain h residue 113 PHE Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 168 CYS Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 305 ASN Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 16 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 379 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 404 optimal weight: 3.9990 chunk 433 optimal weight: 7.9990 chunk 314 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 500 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 84 ASN K 27 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN P 32 HIS ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 24 GLN Y 127 ASN Z 63 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 84823 Z= 0.265 Angle : 0.645 14.669 123619 Z= 0.326 Chirality : 0.039 0.319 15363 Planarity : 0.005 0.065 8630 Dihedral : 23.935 179.901 35078 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 5.73 % Allowed : 20.73 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.12), residues: 4788 helix: 0.38 (0.13), residues: 1540 sheet: -1.28 (0.17), residues: 855 loop : -1.37 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP h 17 HIS 0.007 0.001 HIS h 188 PHE 0.023 0.002 PHE F 226 TYR 0.029 0.002 TYR L 57 ARG 0.007 0.001 ARG b 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 860 time to evaluate : 4.591 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: B 52 LYS cc_start: 0.7575 (tttt) cc_final: 0.6404 (mttp) REVERT: B 94 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7907 (p) REVERT: B 117 ARG cc_start: 0.7280 (mmt90) cc_final: 0.6577 (mmm160) REVERT: B 135 MET cc_start: 0.6149 (mmm) cc_final: 0.5853 (mmt) REVERT: B 174 MET cc_start: 0.8121 (mmm) cc_final: 0.7701 (mmm) REVERT: B 189 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7613 (pt) REVERT: C 38 MET cc_start: 0.7382 (ptp) cc_final: 0.6838 (mpp) REVERT: C 46 LYS cc_start: 0.8646 (mmmm) cc_final: 0.7561 (mtpt) REVERT: C 77 ASP cc_start: 0.7560 (t0) cc_final: 0.7261 (m-30) REVERT: C 82 ARG cc_start: 0.7896 (ttm110) cc_final: 0.6910 (mtp85) REVERT: C 103 MET cc_start: 0.7720 (tmm) cc_final: 0.6877 (tpp) REVERT: C 115 LYS cc_start: 0.7517 (mtmp) cc_final: 0.7173 (mttp) REVERT: C 133 TYR cc_start: 0.6890 (m-80) cc_final: 0.6564 (m-80) REVERT: C 195 LYS cc_start: 0.6625 (mmpt) cc_final: 0.6006 (pttm) REVERT: C 209 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7721 (t70) REVERT: D 68 ARG cc_start: 0.8011 (tpm170) cc_final: 0.7683 (tpp-160) REVERT: D 72 ASP cc_start: 0.6563 (m-30) cc_final: 0.5637 (m-30) REVERT: D 80 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: D 82 TYR cc_start: 0.8322 (m-10) cc_final: 0.8096 (m-10) REVERT: D 92 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6145 (mt-10) REVERT: D 105 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6066 (tp30) REVERT: D 145 LYS cc_start: 0.7957 (mttm) cc_final: 0.7285 (ptpt) REVERT: E 56 GLN cc_start: 0.5544 (tt0) cc_final: 0.5142 (mm-40) REVERT: E 74 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6461 (tm-30) REVERT: E 89 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6098 (mp0) REVERT: E 90 LYS cc_start: 0.7605 (ttpt) cc_final: 0.6562 (tptt) REVERT: E 116 ARG cc_start: 0.6250 (mmt90) cc_final: 0.5763 (mtp180) REVERT: E 117 ARG cc_start: 0.7786 (mmm160) cc_final: 0.6991 (mtt-85) REVERT: E 119 CYS cc_start: 0.7902 (m) cc_final: 0.7638 (m) REVERT: E 143 ARG cc_start: 0.5447 (ttp80) cc_final: 0.4727 (mmm-85) REVERT: E 157 MET cc_start: 0.8138 (mmm) cc_final: 0.7779 (mmm) REVERT: E 207 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6842 (t70) REVERT: F 40 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7729 (mm-30) REVERT: F 67 GLN cc_start: 0.8377 (mt0) cc_final: 0.7873 (mt0) REVERT: F 118 GLU cc_start: 0.7027 (tt0) cc_final: 0.6521 (mm-30) REVERT: F 120 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6772 (tppt) REVERT: F 182 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7982 (tpp) REVERT: F 199 GLU cc_start: 0.7247 (tt0) cc_final: 0.5914 (tp30) REVERT: F 250 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6868 (mt-10) REVERT: G 36 GLN cc_start: 0.7401 (tp40) cc_final: 0.7073 (tp40) REVERT: G 47 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7711 (mmtt) REVERT: G 55 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7250 (mtm110) REVERT: G 106 GLU cc_start: 0.6923 (tt0) cc_final: 0.6364 (tt0) REVERT: G 172 CYS cc_start: 0.7629 (m) cc_final: 0.7336 (m) REVERT: G 198 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7498 (ttm-80) REVERT: H 4 ASN cc_start: 0.6028 (t0) cc_final: 0.5617 (t0) REVERT: H 22 ARG cc_start: 0.6826 (mtm110) cc_final: 0.6196 (ttt-90) REVERT: H 30 LYS cc_start: 0.6923 (mmtm) cc_final: 0.6203 (mmtt) REVERT: H 32 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5508 (mtp) REVERT: H 59 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7658 (mp10) REVERT: H 63 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6752 (mtt) REVERT: H 149 LYS cc_start: 0.5810 (mtmt) cc_final: 0.4831 (mmmt) REVERT: H 154 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7106 (mtm180) REVERT: H 155 GLN cc_start: 0.5355 (mt0) cc_final: 0.5028 (mm-40) REVERT: H 197 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7953 (mt0) REVERT: I 58 LYS cc_start: 0.6699 (mttt) cc_final: 0.6306 (mttm) REVERT: I 113 LYS cc_start: 0.3693 (OUTLIER) cc_final: 0.2047 (mmtm) REVERT: J 28 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8188 (mt-10) REVERT: J 87 ASN cc_start: 0.6189 (t0) cc_final: 0.5819 (t0) REVERT: J 92 ARG cc_start: 0.7258 (tmm-80) cc_final: 0.6863 (mtt180) REVERT: J 157 LYS cc_start: 0.7617 (ttpt) cc_final: 0.7385 (ttpt) REVERT: J 163 GLU cc_start: 0.6912 (tt0) cc_final: 0.6211 (tp30) REVERT: J 191 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: K 66 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7894 (pttt) REVERT: K 79 ARG cc_start: 0.7672 (ppp-140) cc_final: 0.6610 (ttm-80) REVERT: K 103 GLU cc_start: 0.7346 (mp0) cc_final: 0.6941 (mt-10) REVERT: K 135 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.8024 (mp) REVERT: L 5 LYS cc_start: 0.6437 (tppt) cc_final: 0.5876 (ttpp) REVERT: M 45 LYS cc_start: 0.8176 (mptp) cc_final: 0.7836 (mttp) REVERT: M 48 LYS cc_start: 0.7421 (pptt) cc_final: 0.7094 (ptmt) REVERT: M 49 GLU cc_start: 0.7540 (tm-30) cc_final: 0.6607 (mt-10) REVERT: M 93 LEU cc_start: 0.8327 (mt) cc_final: 0.7804 (mm) REVERT: M 103 GLU cc_start: 0.8283 (pt0) cc_final: 0.7784 (pt0) REVERT: M 121 GLN cc_start: 0.5979 (mm-40) cc_final: 0.5572 (mp10) REVERT: N 23 LYS cc_start: 0.6275 (mttt) cc_final: 0.5467 (mtmt) REVERT: N 63 LYS cc_start: 0.5948 (ttmt) cc_final: 0.5559 (tptp) REVERT: O 38 TYR cc_start: 0.6871 (m-80) cc_final: 0.6644 (m-80) REVERT: O 99 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7647 (mmm160) REVERT: O 110 ASP cc_start: 0.7984 (t0) cc_final: 0.7673 (t0) REVERT: O 140 LYS cc_start: 0.7777 (tttm) cc_final: 0.7209 (ttmm) REVERT: P 51 GLU cc_start: 0.7744 (tp30) cc_final: 0.7401 (tp30) REVERT: P 63 LYS cc_start: 0.5886 (mmpt) cc_final: 0.5570 (mmmt) REVERT: P 128 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6835 (mmt-90) REVERT: P 135 ILE cc_start: 0.8402 (mt) cc_final: 0.8150 (mm) REVERT: Q 31 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5707 (tt0) REVERT: Q 41 GLN cc_start: 0.7772 (mp10) cc_final: 0.7341 (mp10) REVERT: Q 72 LYS cc_start: 0.7124 (mttt) cc_final: 0.6322 (ptmt) REVERT: Q 89 MET cc_start: 0.7568 (ttm) cc_final: 0.7340 (ttp) REVERT: Q 93 MET cc_start: 0.7189 (ttp) cc_final: 0.6532 (mtp) REVERT: Q 118 GLU cc_start: 0.7140 (tt0) cc_final: 0.6720 (mt-10) REVERT: R 98 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7375 (tppt) REVERT: R 106 LYS cc_start: 0.6893 (ttpm) cc_final: 0.6506 (tttp) REVERT: R 146 ARG cc_start: 0.5646 (mpt90) cc_final: 0.4648 (mtm110) REVERT: S 11 LYS cc_start: 0.7672 (mttt) cc_final: 0.7271 (mmtt) REVERT: S 93 GLN cc_start: 0.6118 (mt0) cc_final: 0.5511 (tp40) REVERT: S 107 LYS cc_start: 0.6162 (tmmt) cc_final: 0.5715 (ttmm) REVERT: S 111 PHE cc_start: 0.5328 (OUTLIER) cc_final: 0.4981 (m-80) REVERT: S 118 GLN cc_start: 0.6112 (tt0) cc_final: 0.5133 (tm-30) REVERT: S 130 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7545 (p) REVERT: T 46 ARG cc_start: 0.7410 (mmt180) cc_final: 0.6393 (tpt-90) REVERT: T 54 LYS cc_start: 0.6815 (mttt) cc_final: 0.6498 (mtpt) REVERT: T 63 GLU cc_start: 0.7131 (mp0) cc_final: 0.6888 (mp0) REVERT: T 94 LYS cc_start: 0.6362 (mttp) cc_final: 0.5969 (mmmt) REVERT: T 115 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6314 (mttt) REVERT: U 8 ASP cc_start: 0.7095 (t0) cc_final: 0.6804 (m-30) REVERT: U 13 GLU cc_start: 0.8041 (pt0) cc_final: 0.7411 (pm20) REVERT: U 133 ARG cc_start: 0.7093 (mtp180) cc_final: 0.6594 (mtm-85) REVERT: V 20 ILE cc_start: 0.7318 (tt) cc_final: 0.6512 (mt) REVERT: V 21 ARG cc_start: 0.6004 (ttt90) cc_final: 0.5290 (mmt-90) REVERT: V 30 LYS cc_start: 0.7712 (ptmt) cc_final: 0.7107 (mmmt) REVERT: V 44 LYS cc_start: 0.6434 (mptm) cc_final: 0.5933 (mtpt) REVERT: W 45 ARG cc_start: 0.6923 (mtt180) cc_final: 0.6627 (mtm-85) REVERT: W 50 SER cc_start: 0.5775 (OUTLIER) cc_final: 0.5047 (p) REVERT: X 13 SER cc_start: 0.8683 (t) cc_final: 0.8255 (m) REVERT: X 87 GLU cc_start: 0.8231 (tp30) cc_final: 0.7726 (mm-30) REVERT: Y 37 LYS cc_start: 0.7156 (tptt) cc_final: 0.6643 (tmtt) REVERT: Y 95 GLU cc_start: 0.7922 (tt0) cc_final: 0.7575 (tt0) REVERT: Y 114 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: Y 139 GLU cc_start: 0.5645 (mm-30) cc_final: 0.4829 (mp0) REVERT: Y 140 ARG cc_start: 0.5816 (mtp-110) cc_final: 0.4772 (mtp180) REVERT: Z 8 ARG cc_start: 0.7399 (mtt-85) cc_final: 0.6066 (ttt90) REVERT: Z 15 ASN cc_start: 0.7312 (t0) cc_final: 0.6957 (t0) REVERT: Z 39 GLU cc_start: 0.7725 (mt-10) cc_final: 0.6959 (mp0) REVERT: Z 42 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7111 (pt0) REVERT: Z 48 TYR cc_start: 0.6522 (m-80) cc_final: 0.6009 (m-80) REVERT: Z 106 GLN cc_start: 0.7748 (mt0) cc_final: 0.7252 (mm110) REVERT: a 51 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6203 (t0) REVERT: a 60 LYS cc_start: 0.7131 (mmtt) cc_final: 0.6916 (mttt) REVERT: a 92 LEU cc_start: 0.7830 (tp) cc_final: 0.7546 (tp) REVERT: b 89 ARG cc_start: 0.6608 (mtp-110) cc_final: 0.6038 (mtt180) REVERT: b 94 ASP cc_start: 0.6742 (m-30) cc_final: 0.6471 (m-30) REVERT: c 36 LYS cc_start: 0.5488 (pttm) cc_final: 0.5116 (tptp) REVERT: c 72 ARG cc_start: 0.6282 (mtm180) cc_final: 0.6019 (ttm170) REVERT: d 54 ASP cc_start: 0.7420 (p0) cc_final: 0.7122 (p0) REVERT: e 8 TRP cc_start: 0.8246 (t-100) cc_final: 0.7539 (t-100) REVERT: e 13 LYS cc_start: 0.7897 (mttt) cc_final: 0.6914 (mmtm) REVERT: e 38 MET cc_start: 0.7553 (ttm) cc_final: 0.7206 (ttm) REVERT: e 48 LYS cc_start: 0.7647 (tppp) cc_final: 0.7391 (ttpt) REVERT: f 96 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7782 (mm-30) REVERT: f 126 LYS cc_start: 0.6215 (mtmt) cc_final: 0.5875 (pttt) REVERT: h 8 ARG cc_start: 0.5195 (ttt-90) cc_final: 0.4530 (tpt90) REVERT: h 15 ASN cc_start: 0.6875 (m-40) cc_final: 0.6525 (m-40) REVERT: h 30 MET cc_start: 0.4324 (tmm) cc_final: 0.3732 (mmt) REVERT: h 57 ARG cc_start: 0.7131 (tpp80) cc_final: 0.6520 (mmm-85) REVERT: h 89 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6793 (tt) REVERT: h 113 PHE cc_start: 0.5534 (OUTLIER) cc_final: 0.3823 (t80) REVERT: h 120 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6301 (pt) REVERT: h 177 TRP cc_start: 0.6200 (m100) cc_final: 0.5667 (m100) REVERT: h 217 MET cc_start: 0.5311 (mtt) cc_final: 0.4954 (ttm) REVERT: h 235 ILE cc_start: 0.7468 (tt) cc_final: 0.7221 (tt) REVERT: h 264 LYS cc_start: 0.6326 (mptt) cc_final: 0.5568 (ttpt) REVERT: h 268 ASP cc_start: 0.5030 (OUTLIER) cc_final: 0.4020 (p0) REVERT: h 305 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6381 (m-40) REVERT: n 1 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.6105 (tmm) REVERT: n 21 ARG cc_start: 0.6732 (ttt90) cc_final: 0.6288 (mtp180) outliers start: 240 outliers final: 188 residues processed: 1023 average time/residue: 0.8344 time to fit residues: 1407.1377 Evaluate side-chains 1053 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 837 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 57 LEU Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 43 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 111 PHE Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain U residue 124 THR Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 41 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 CYS Chi-restraints excluded: chain V residue 84 ILE Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain X residue 24 GLN Chi-restraints excluded: chain X residue 27 ILE Chi-restraints excluded: chain X residue 32 LYS Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 15 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 87 ASN Chi-restraints excluded: chain Y residue 97 ASN Chi-restraints excluded: chain Y residue 98 ASP Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 114 ASP Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Y residue 127 ASN Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 83 LEU Chi-restraints excluded: chain b residue 15 ARG Chi-restraints excluded: chain b residue 25 ASN Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain g residue 87 THR Chi-restraints excluded: chain h residue 29 ASP Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 104 HIS Chi-restraints excluded: chain h residue 113 PHE Chi-restraints excluded: chain h residue 120 ILE Chi-restraints excluded: chain h residue 126 ASP Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 168 CYS Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 285 GLN Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 305 ASN Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 16 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 1.9990 chunk 609 optimal weight: 9.9990 chunk 556 optimal weight: 0.0270 chunk 592 optimal weight: 2.9990 chunk 356 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 465 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 535 optimal weight: 0.6980 chunk 560 optimal weight: 3.9990 chunk 590 optimal weight: 6.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 GLN G 118 ASN G 203 ASN J 84 ASN J 138 ASN K 27 GLN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS X 15 ASN X 24 GLN Y 127 ASN Z 63 HIS h 117 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 84823 Z= 0.141 Angle : 0.567 15.190 123619 Z= 0.287 Chirality : 0.035 0.310 15363 Planarity : 0.004 0.064 8630 Dihedral : 23.824 179.440 35077 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 4.25 % Allowed : 22.28 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4788 helix: 0.69 (0.13), residues: 1564 sheet: -1.09 (0.17), residues: 858 loop : -1.21 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP h 177 HIS 0.007 0.001 HIS Q 79 PHE 0.027 0.001 PHE J 197 TYR 0.022 0.001 TYR T 40 ARG 0.008 0.000 ARG M 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 908 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.7547 (tttt) cc_final: 0.6371 (mttp) REVERT: B 117 ARG cc_start: 0.7183 (mmt90) cc_final: 0.6520 (mmm160) REVERT: B 135 MET cc_start: 0.6303 (mmm) cc_final: 0.5956 (mmt) REVERT: B 166 LYS cc_start: 0.7793 (tttt) cc_final: 0.7340 (ttpp) REVERT: B 174 MET cc_start: 0.7853 (mmm) cc_final: 0.7476 (mmm) REVERT: B 189 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7497 (pt) REVERT: C 38 MET cc_start: 0.7191 (ptp) cc_final: 0.6744 (mpp) REVERT: C 46 LYS cc_start: 0.8631 (mmmm) cc_final: 0.7591 (mtpt) REVERT: C 69 VAL cc_start: 0.8866 (t) cc_final: 0.8542 (p) REVERT: C 82 ARG cc_start: 0.7830 (ttm110) cc_final: 0.6619 (mtp85) REVERT: C 103 MET cc_start: 0.7601 (tmm) cc_final: 0.6776 (tpp) REVERT: C 115 LYS cc_start: 0.7562 (mtmp) cc_final: 0.7186 (mttp) REVERT: C 133 TYR cc_start: 0.6813 (m-80) cc_final: 0.6555 (m-80) REVERT: C 195 LYS cc_start: 0.6744 (mmpt) cc_final: 0.6096 (pttm) REVERT: C 209 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.6789 (t70) REVERT: C 211 PHE cc_start: 0.7229 (m-80) cc_final: 0.6943 (m-80) REVERT: D 68 ARG cc_start: 0.7951 (tpm170) cc_final: 0.7655 (tpp-160) REVERT: D 72 ASP cc_start: 0.6620 (m-30) cc_final: 0.5472 (m-30) REVERT: D 80 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7331 (pt0) REVERT: D 105 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6049 (tp30) REVERT: D 145 LYS cc_start: 0.7833 (mttm) cc_final: 0.6993 (ptpt) REVERT: D 146 GLU cc_start: 0.7238 (pm20) cc_final: 0.6579 (mp0) REVERT: D 251 LEU cc_start: 0.7434 (tm) cc_final: 0.6964 (mt) REVERT: E 56 GLN cc_start: 0.5586 (tt0) cc_final: 0.5155 (mm-40) REVERT: E 74 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6373 (tm-30) REVERT: E 89 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: E 90 LYS cc_start: 0.7607 (ttpt) cc_final: 0.6642 (tptt) REVERT: E 116 ARG cc_start: 0.6367 (mmt90) cc_final: 0.5866 (mtp180) REVERT: E 117 ARG cc_start: 0.7718 (mmm160) cc_final: 0.6874 (mtp85) REVERT: E 119 CYS cc_start: 0.7867 (m) cc_final: 0.7568 (m) REVERT: E 143 ARG cc_start: 0.4931 (ttp80) cc_final: 0.4214 (mmm-85) REVERT: E 157 MET cc_start: 0.8118 (mmm) cc_final: 0.7746 (mmm) REVERT: F 40 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7775 (mm-30) REVERT: F 67 GLN cc_start: 0.8519 (mt0) cc_final: 0.8014 (mt0) REVERT: F 100 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7317 (ttm110) REVERT: F 115 THR cc_start: 0.7027 (OUTLIER) cc_final: 0.6653 (t) REVERT: F 118 GLU cc_start: 0.6997 (tt0) cc_final: 0.6397 (mm-30) REVERT: F 120 LYS cc_start: 0.7305 (ttmp) cc_final: 0.6800 (tppt) REVERT: F 181 CYS cc_start: 0.8138 (t) cc_final: 0.7911 (t) REVERT: F 182 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7743 (tpp) REVERT: F 199 GLU cc_start: 0.7258 (tt0) cc_final: 0.5949 (tp30) REVERT: F 212 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7228 (m-30) REVERT: G 47 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7563 (mmtt) REVERT: G 55 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7266 (mtm110) REVERT: G 76 MET cc_start: 0.8396 (mmm) cc_final: 0.7541 (tpp) REVERT: G 106 GLU cc_start: 0.6879 (tt0) cc_final: 0.6378 (tt0) REVERT: G 198 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7522 (ttm-80) REVERT: H 4 ASN cc_start: 0.5196 (t0) cc_final: 0.4892 (t0) REVERT: H 14 LYS cc_start: 0.6236 (ttpt) cc_final: 0.5615 (tttm) REVERT: H 20 ASP cc_start: 0.6823 (t70) cc_final: 0.6479 (t70) REVERT: H 22 ARG cc_start: 0.6938 (mtm110) cc_final: 0.6403 (ttt-90) REVERT: H 30 LYS cc_start: 0.6734 (mmtm) cc_final: 0.5982 (mmtt) REVERT: H 32 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5410 (mtp) REVERT: H 63 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6366 (mtt) REVERT: H 149 LYS cc_start: 0.5778 (mtmt) cc_final: 0.4799 (mmmt) REVERT: H 154 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7069 (mtm180) REVERT: H 155 GLN cc_start: 0.5332 (mt0) cc_final: 0.5098 (mm-40) REVERT: H 197 GLN cc_start: 0.8374 (tp-100) cc_final: 0.7990 (mt0) REVERT: I 58 LYS cc_start: 0.6547 (mttt) cc_final: 0.6158 (mttm) REVERT: I 83 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5847 (mt) REVERT: I 113 LYS cc_start: 0.3607 (OUTLIER) cc_final: 0.2124 (mmtm) REVERT: I 160 LYS cc_start: 0.5437 (tptp) cc_final: 0.5227 (tptm) REVERT: J 28 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8212 (mt-10) REVERT: J 92 ARG cc_start: 0.7048 (tmm-80) cc_final: 0.6722 (ptp-170) REVERT: J 117 TYR cc_start: 0.7137 (m-80) cc_final: 0.6825 (m-10) REVERT: J 153 LYS cc_start: 0.6899 (ttpt) cc_final: 0.6665 (mtmm) REVERT: J 157 LYS cc_start: 0.7625 (ttpt) cc_final: 0.7397 (ttpt) REVERT: J 163 GLU cc_start: 0.6588 (tt0) cc_final: 0.5966 (tp30) REVERT: J 191 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: K 27 GLN cc_start: 0.7503 (tp40) cc_final: 0.7080 (pt0) REVERT: K 66 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7839 (pttt) REVERT: K 79 ARG cc_start: 0.7736 (ppp-140) cc_final: 0.6705 (ttm-80) REVERT: K 94 LEU cc_start: 0.7245 (pt) cc_final: 0.6648 (tp) REVERT: K 103 GLU cc_start: 0.7347 (mp0) cc_final: 0.6823 (mt-10) REVERT: K 135 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7945 (mp) REVERT: L 5 LYS cc_start: 0.6367 (tppt) cc_final: 0.5777 (ttpp) REVERT: M 45 LYS cc_start: 0.8235 (mptp) cc_final: 0.7992 (mttp) REVERT: M 48 LYS cc_start: 0.7399 (pptt) cc_final: 0.7082 (ptmt) REVERT: M 49 GLU cc_start: 0.7533 (tm-30) cc_final: 0.6565 (mt-10) REVERT: M 68 ILE cc_start: 0.7857 (mt) cc_final: 0.7575 (mt) REVERT: M 93 LEU cc_start: 0.8335 (mt) cc_final: 0.7912 (mm) REVERT: M 97 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7298 (ttt180) REVERT: M 103 GLU cc_start: 0.8130 (pt0) cc_final: 0.7632 (pt0) REVERT: M 108 ASN cc_start: 0.7176 (p0) cc_final: 0.6602 (p0) REVERT: M 121 GLN cc_start: 0.6037 (mm-40) cc_final: 0.5599 (mp10) REVERT: N 23 LYS cc_start: 0.6207 (mttt) cc_final: 0.5421 (mtmt) REVERT: N 43 ASP cc_start: 0.5589 (OUTLIER) cc_final: 0.5382 (t70) REVERT: N 63 LYS cc_start: 0.6198 (ttmt) cc_final: 0.5674 (tptp) REVERT: O 38 TYR cc_start: 0.6786 (m-80) cc_final: 0.6541 (m-80) REVERT: O 99 ARG cc_start: 0.7943 (mtp180) cc_final: 0.7714 (mmm160) REVERT: O 140 LYS cc_start: 0.7831 (tttm) cc_final: 0.7254 (ttmm) REVERT: P 51 GLU cc_start: 0.7648 (tp30) cc_final: 0.7177 (tp30) REVERT: P 63 LYS cc_start: 0.5858 (mmpt) cc_final: 0.5556 (mmmt) REVERT: P 128 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6920 (mmt-90) REVERT: P 135 ILE cc_start: 0.8482 (mt) cc_final: 0.8236 (mm) REVERT: Q 15 PHE cc_start: 0.5807 (p90) cc_final: 0.5300 (p90) REVERT: Q 31 GLU cc_start: 0.6187 (mt-10) cc_final: 0.5617 (tt0) REVERT: Q 41 GLN cc_start: 0.7711 (mp10) cc_final: 0.7319 (mp10) REVERT: Q 58 LYS cc_start: 0.6429 (mmtt) cc_final: 0.5505 (mptt) REVERT: Q 61 ARG cc_start: 0.6703 (mtt90) cc_final: 0.6422 (mmp80) REVERT: Q 62 LYS cc_start: 0.5800 (mtpm) cc_final: 0.5116 (mptt) REVERT: Q 72 LYS cc_start: 0.7104 (mttt) cc_final: 0.6333 (ptmt) REVERT: Q 93 MET cc_start: 0.7134 (ttp) cc_final: 0.6391 (mtp) REVERT: Q 108 LYS cc_start: 0.7063 (ptpt) cc_final: 0.6229 (mmmt) REVERT: Q 118 GLU cc_start: 0.7093 (tt0) cc_final: 0.6671 (mt-10) REVERT: R 39 LEU cc_start: 0.7587 (mt) cc_final: 0.7276 (tp) REVERT: R 98 LYS cc_start: 0.7749 (ttmt) cc_final: 0.7164 (tppt) REVERT: R 106 LYS cc_start: 0.6962 (ttpm) cc_final: 0.6387 (tttm) REVERT: R 110 ASP cc_start: 0.7476 (m-30) cc_final: 0.7057 (m-30) REVERT: R 146 ARG cc_start: 0.5738 (mpt90) cc_final: 0.4798 (mtm110) REVERT: S 11 LYS cc_start: 0.7750 (mttt) cc_final: 0.7340 (mmtt) REVERT: S 93 GLN cc_start: 0.6070 (mt0) cc_final: 0.5179 (mm110) REVERT: S 107 LYS cc_start: 0.5409 (tmmt) cc_final: 0.5024 (ttmm) REVERT: S 118 GLN cc_start: 0.6245 (tt0) cc_final: 0.5588 (tm-30) REVERT: S 130 THR cc_start: 0.7827 (m) cc_final: 0.7585 (p) REVERT: T 7 GLU cc_start: 0.6008 (mp0) cc_final: 0.5368 (pm20) REVERT: T 46 ARG cc_start: 0.7355 (mmt180) cc_final: 0.6336 (tpt-90) REVERT: T 54 LYS cc_start: 0.6740 (mttt) cc_final: 0.6462 (mtpt) REVERT: T 63 GLU cc_start: 0.7226 (mp0) cc_final: 0.6985 (mp0) REVERT: T 94 LYS cc_start: 0.6287 (mttp) cc_final: 0.5894 (mmmt) REVERT: T 115 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6306 (mttt) REVERT: U 8 ASP cc_start: 0.7072 (t0) cc_final: 0.6762 (m-30) REVERT: U 108 GLU cc_start: 0.7835 (tt0) cc_final: 0.7141 (mt-10) REVERT: U 112 MET cc_start: 0.7626 (mtt) cc_final: 0.7421 (mtt) REVERT: U 115 LYS cc_start: 0.6492 (mmtp) cc_final: 0.6253 (tppt) REVERT: U 133 ARG cc_start: 0.7232 (mtp180) cc_final: 0.6838 (mtm-85) REVERT: V 20 ILE cc_start: 0.7288 (tt) cc_final: 0.6433 (mt) REVERT: V 21 ARG cc_start: 0.5993 (ttt90) cc_final: 0.5241 (mmt-90) REVERT: V 30 LYS cc_start: 0.7595 (ptmt) cc_final: 0.6912 (mmmt) REVERT: V 44 LYS cc_start: 0.6527 (mptm) cc_final: 0.6032 (mtpt) REVERT: W 45 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6726 (mtm-85) REVERT: X 13 SER cc_start: 0.8648 (t) cc_final: 0.8269 (m) REVERT: X 87 GLU cc_start: 0.8227 (tp30) cc_final: 0.7343 (mt-10) REVERT: X 115 GLU cc_start: 0.8488 (tt0) cc_final: 0.7721 (tp30) REVERT: Y 37 LYS cc_start: 0.7181 (tptt) cc_final: 0.6664 (tmtt) REVERT: Y 95 GLU cc_start: 0.7850 (tt0) cc_final: 0.7490 (tt0) REVERT: Y 114 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: Y 139 GLU cc_start: 0.5603 (mm-30) cc_final: 0.4780 (mp0) REVERT: Y 140 ARG cc_start: 0.5746 (mtp-110) cc_final: 0.4725 (mtp180) REVERT: Z 8 ARG cc_start: 0.7302 (mtt-85) cc_final: 0.6024 (ttt90) REVERT: Z 15 ASN cc_start: 0.7261 (t0) cc_final: 0.6857 (t0) REVERT: Z 39 GLU cc_start: 0.7757 (mt-10) cc_final: 0.6779 (mp0) REVERT: Z 42 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7166 (pt0) REVERT: Z 56 PHE cc_start: 0.8445 (m-80) cc_final: 0.8181 (m-10) REVERT: Z 106 GLN cc_start: 0.7499 (mt0) cc_final: 0.7251 (mm110) REVERT: a 56 ASP cc_start: 0.7499 (m-30) cc_final: 0.7184 (m-30) REVERT: a 92 LEU cc_start: 0.7825 (tp) cc_final: 0.7536 (tp) REVERT: b 89 ARG cc_start: 0.6676 (mtp-110) cc_final: 0.6169 (mtt180) REVERT: b 94 ASP cc_start: 0.6610 (m-30) cc_final: 0.6373 (m-30) REVERT: c 36 LYS cc_start: 0.5527 (pttm) cc_final: 0.5217 (tptp) REVERT: c 72 ARG cc_start: 0.6197 (mtm180) cc_final: 0.5801 (ttm170) REVERT: d 13 ARG cc_start: 0.7288 (ttm170) cc_final: 0.6565 (mtt180) REVERT: d 33 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7749 (mt-10) REVERT: d 54 ASP cc_start: 0.6963 (p0) cc_final: 0.6667 (p0) REVERT: d 58 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6353 (mt) REVERT: e 8 TRP cc_start: 0.7799 (t-100) cc_final: 0.7144 (t-100) REVERT: e 13 LYS cc_start: 0.7681 (mttt) cc_final: 0.6795 (mmtm) REVERT: e 38 MET cc_start: 0.7445 (ttm) cc_final: 0.7242 (ttm) REVERT: e 48 LYS cc_start: 0.7693 (tppp) cc_final: 0.7366 (ttpt) REVERT: f 96 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7702 (mm-30) REVERT: f 126 LYS cc_start: 0.6210 (mtmt) cc_final: 0.5913 (pttt) REVERT: g 104 LYS cc_start: 0.5500 (tptt) cc_final: 0.4893 (ptmt) REVERT: h 8 ARG cc_start: 0.5150 (ttt-90) cc_final: 0.4428 (tpt90) REVERT: h 15 ASN cc_start: 0.6795 (m-40) cc_final: 0.6410 (m-40) REVERT: h 30 MET cc_start: 0.4366 (tmm) cc_final: 0.3614 (mmt) REVERT: h 57 ARG cc_start: 0.7162 (tpp80) cc_final: 0.6548 (mmm-85) REVERT: h 177 TRP cc_start: 0.6171 (m100) cc_final: 0.5640 (m100) REVERT: h 217 MET cc_start: 0.5395 (mtt) cc_final: 0.4731 (ttm) REVERT: h 264 LYS cc_start: 0.6473 (mptt) cc_final: 0.5684 (ttpt) REVERT: h 269 GLU cc_start: 0.5555 (tt0) cc_final: 0.5164 (tp30) REVERT: h 305 ASN cc_start: 0.6454 (OUTLIER) cc_final: 0.5945 (m-40) REVERT: n 1 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6860 (ttt) REVERT: n 15 ARG cc_start: 0.7054 (ttp-170) cc_final: 0.6668 (ttp-170) REVERT: n 21 ARG cc_start: 0.6760 (ttt90) cc_final: 0.5957 (tpt90) outliers start: 178 outliers final: 124 residues processed: 1020 average time/residue: 0.8432 time to fit residues: 1407.2993 Evaluate side-chains 1001 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 856 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain S residue 43 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 28 ASN Chi-restraints excluded: chain V residue 41 ARG Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain X residue 27 ILE Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 87 ASN Chi-restraints excluded: chain Y residue 114 ASP Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Y residue 127 ASN Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 104 HIS Chi-restraints excluded: chain h residue 113 PHE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 168 CYS Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 305 ASN Chi-restraints excluded: chain n residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 7.9990 chunk 626 optimal weight: 10.0000 chunk 382 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 435 optimal weight: 0.3980 chunk 657 optimal weight: 20.0000 chunk 605 optimal weight: 20.0000 chunk 523 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 404 optimal weight: 6.9990 chunk 321 optimal weight: 2.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN G 203 ASN J 99 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN P 32 HIS ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 HIS ** b 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 84823 Z= 0.336 Angle : 0.699 14.548 123619 Z= 0.351 Chirality : 0.042 0.325 15363 Planarity : 0.005 0.078 8630 Dihedral : 23.931 179.806 35074 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 4.25 % Allowed : 22.69 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 4788 helix: 0.38 (0.13), residues: 1537 sheet: -1.18 (0.17), residues: 846 loop : -1.32 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP h 17 HIS 0.007 0.001 HIS L 66 PHE 0.030 0.002 PHE B 203 TYR 0.021 0.002 TYR D 82 ARG 0.009 0.001 ARG b 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 840 time to evaluate : 5.105 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: B 52 LYS cc_start: 0.7578 (tttt) cc_final: 0.6393 (mttp) REVERT: B 94 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7948 (p) REVERT: B 117 ARG cc_start: 0.7477 (mmt90) cc_final: 0.6719 (mmm160) REVERT: B 134 LEU cc_start: 0.7643 (mt) cc_final: 0.7420 (mt) REVERT: B 135 MET cc_start: 0.6298 (mmm) cc_final: 0.5961 (mmt) REVERT: B 174 MET cc_start: 0.8145 (mmm) cc_final: 0.7802 (mmm) REVERT: C 38 MET cc_start: 0.7329 (ptp) cc_final: 0.6844 (mpp) REVERT: C 46 LYS cc_start: 0.8644 (mmmm) cc_final: 0.7576 (mtpt) REVERT: C 77 ASP cc_start: 0.7591 (t0) cc_final: 0.7278 (m-30) REVERT: C 82 ARG cc_start: 0.7876 (ttm110) cc_final: 0.6842 (mtp85) REVERT: C 115 LYS cc_start: 0.7426 (mtmp) cc_final: 0.7129 (mttp) REVERT: C 133 TYR cc_start: 0.6872 (m-80) cc_final: 0.6552 (m-80) REVERT: C 195 LYS cc_start: 0.6581 (mmpt) cc_final: 0.5958 (pttm) REVERT: C 209 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7811 (t70) REVERT: D 68 ARG cc_start: 0.7985 (tpm170) cc_final: 0.7540 (tpp-160) REVERT: D 72 ASP cc_start: 0.6445 (m-30) cc_final: 0.5190 (m-30) REVERT: D 105 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6075 (tp30) REVERT: D 145 LYS cc_start: 0.7910 (mttm) cc_final: 0.7248 (ptpt) REVERT: D 274 MET cc_start: 0.5076 (mmm) cc_final: 0.4423 (mmm) REVERT: E 56 GLN cc_start: 0.5666 (tt0) cc_final: 0.5267 (mm-40) REVERT: E 74 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6192 (tm-30) REVERT: E 89 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: E 90 LYS cc_start: 0.7675 (ttpt) cc_final: 0.6600 (tptt) REVERT: E 116 ARG cc_start: 0.6314 (mmt90) cc_final: 0.5801 (mtp180) REVERT: E 117 ARG cc_start: 0.7760 (mmm160) cc_final: 0.6988 (mtt-85) REVERT: E 119 CYS cc_start: 0.7902 (m) cc_final: 0.7632 (m) REVERT: E 143 ARG cc_start: 0.5379 (ttp80) cc_final: 0.4705 (mmm-85) REVERT: E 157 MET cc_start: 0.8125 (mmm) cc_final: 0.7771 (mmm) REVERT: F 40 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7795 (mm-30) REVERT: F 118 GLU cc_start: 0.7044 (tt0) cc_final: 0.6535 (mm-30) REVERT: F 120 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6758 (tppt) REVERT: F 182 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7955 (tpp) REVERT: F 199 GLU cc_start: 0.7243 (tt0) cc_final: 0.5930 (tp30) REVERT: F 212 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: G 36 GLN cc_start: 0.7405 (tp40) cc_final: 0.7071 (tp40) REVERT: G 47 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7726 (mmtt) REVERT: G 55 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7292 (mtm110) REVERT: G 76 MET cc_start: 0.8353 (mmm) cc_final: 0.7279 (tpp) REVERT: G 106 GLU cc_start: 0.7041 (tt0) cc_final: 0.6482 (tt0) REVERT: G 198 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7475 (ttm-80) REVERT: H 4 ASN cc_start: 0.5769 (t0) cc_final: 0.5387 (t0) REVERT: H 14 LYS cc_start: 0.6294 (ttpt) cc_final: 0.5759 (tttm) REVERT: H 22 ARG cc_start: 0.6802 (mtm110) cc_final: 0.6209 (ttt-90) REVERT: H 30 LYS cc_start: 0.6928 (mmtm) cc_final: 0.6167 (mmtt) REVERT: H 32 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.5562 (mtp) REVERT: H 59 GLN cc_start: 0.7979 (mp10) cc_final: 0.7364 (mp10) REVERT: H 63 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6799 (mtt) REVERT: H 149 LYS cc_start: 0.5836 (mtmt) cc_final: 0.4844 (mmmt) REVERT: H 154 ARG cc_start: 0.7704 (mtt-85) cc_final: 0.7056 (mtm180) REVERT: H 155 GLN cc_start: 0.5360 (mt0) cc_final: 0.5015 (mm-40) REVERT: H 197 GLN cc_start: 0.8439 (tp-100) cc_final: 0.7966 (mt0) REVERT: I 58 LYS cc_start: 0.6629 (mttt) cc_final: 0.6246 (mttm) REVERT: I 113 LYS cc_start: 0.3804 (OUTLIER) cc_final: 0.2153 (mmtm) REVERT: J 28 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8134 (mt-10) REVERT: J 87 ASN cc_start: 0.6752 (t0) cc_final: 0.6387 (t0) REVERT: J 92 ARG cc_start: 0.7269 (tmm-80) cc_final: 0.6867 (mtt180) REVERT: J 153 LYS cc_start: 0.6985 (ttpt) cc_final: 0.6655 (mttm) REVERT: J 163 GLU cc_start: 0.6905 (tt0) cc_final: 0.6244 (tp30) REVERT: J 191 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: K 27 GLN cc_start: 0.7264 (tp40) cc_final: 0.6933 (pt0) REVERT: K 66 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7909 (pttt) REVERT: K 79 ARG cc_start: 0.7587 (ppp-140) cc_final: 0.6618 (ttm-80) REVERT: K 103 GLU cc_start: 0.7383 (mp0) cc_final: 0.6884 (mt-10) REVERT: K 135 ILE cc_start: 0.8271 (mt) cc_final: 0.8059 (mp) REVERT: L 5 LYS cc_start: 0.6408 (tppt) cc_final: 0.5773 (ttpp) REVERT: L 12 TYR cc_start: 0.6394 (m-80) cc_final: 0.6083 (m-80) REVERT: M 48 LYS cc_start: 0.7426 (pptt) cc_final: 0.7088 (ptmt) REVERT: M 49 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6619 (mt-10) REVERT: M 93 LEU cc_start: 0.8246 (mt) cc_final: 0.7635 (mm) REVERT: M 97 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7490 (ttt180) REVERT: M 121 GLN cc_start: 0.5982 (mm-40) cc_final: 0.5577 (mp10) REVERT: N 23 LYS cc_start: 0.6374 (mttt) cc_final: 0.5542 (mtmt) REVERT: N 63 LYS cc_start: 0.5898 (ttmt) cc_final: 0.5455 (tptp) REVERT: O 38 TYR cc_start: 0.6830 (m-80) cc_final: 0.6562 (m-80) REVERT: O 99 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7666 (mmm160) REVERT: O 110 ASP cc_start: 0.8041 (t0) cc_final: 0.7669 (t0) REVERT: O 119 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6714 (mt-10) REVERT: O 140 LYS cc_start: 0.7525 (tttm) cc_final: 0.6979 (ttmm) REVERT: P 28 PHE cc_start: 0.7796 (m-80) cc_final: 0.7487 (m-80) REVERT: P 51 GLU cc_start: 0.7697 (tp30) cc_final: 0.7340 (tp30) REVERT: P 63 LYS cc_start: 0.5900 (mmpt) cc_final: 0.5639 (mmmt) REVERT: P 72 TYR cc_start: 0.8032 (t80) cc_final: 0.7809 (t80) REVERT: P 135 ILE cc_start: 0.8414 (mt) cc_final: 0.8154 (mm) REVERT: Q 15 PHE cc_start: 0.5716 (p90) cc_final: 0.5410 (p90) REVERT: Q 31 GLU cc_start: 0.6125 (mt-10) cc_final: 0.5897 (tt0) REVERT: Q 41 GLN cc_start: 0.7770 (mp10) cc_final: 0.7342 (mp10) REVERT: Q 61 ARG cc_start: 0.6710 (mtt90) cc_final: 0.6501 (mmp80) REVERT: Q 72 LYS cc_start: 0.7160 (mttt) cc_final: 0.6402 (ptmt) REVERT: Q 93 MET cc_start: 0.7143 (ttp) cc_final: 0.6311 (mtp) REVERT: Q 118 GLU cc_start: 0.7053 (tt0) cc_final: 0.6682 (mt-10) REVERT: R 98 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7456 (tppt) REVERT: R 106 LYS cc_start: 0.6899 (ttpm) cc_final: 0.6541 (tttm) REVERT: R 146 ARG cc_start: 0.5642 (mpt90) cc_final: 0.4781 (mtm110) REVERT: S 11 LYS cc_start: 0.7731 (mttt) cc_final: 0.7322 (mmtt) REVERT: S 93 GLN cc_start: 0.6121 (mt0) cc_final: 0.5517 (tp40) REVERT: S 107 LYS cc_start: 0.5973 (tmmt) cc_final: 0.5562 (ttmm) REVERT: S 118 GLN cc_start: 0.6065 (tt0) cc_final: 0.5115 (tm-30) REVERT: S 130 THR cc_start: 0.7755 (m) cc_final: 0.7544 (p) REVERT: T 46 ARG cc_start: 0.7435 (mmt180) cc_final: 0.6383 (tpt-90) REVERT: T 54 LYS cc_start: 0.6782 (mttt) cc_final: 0.6476 (mtpt) REVERT: T 63 GLU cc_start: 0.7117 (mp0) cc_final: 0.6864 (mp0) REVERT: T 94 LYS cc_start: 0.6376 (mttp) cc_final: 0.5991 (mmmt) REVERT: T 115 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6249 (mttt) REVERT: U 8 ASP cc_start: 0.7140 (t0) cc_final: 0.6800 (m-30) REVERT: U 108 GLU cc_start: 0.7916 (tt0) cc_final: 0.7190 (mt-10) REVERT: U 115 LYS cc_start: 0.6318 (mmtp) cc_final: 0.6012 (mmtp) REVERT: U 133 ARG cc_start: 0.7265 (mtp180) cc_final: 0.6737 (mtm-85) REVERT: V 20 ILE cc_start: 0.7345 (tt) cc_final: 0.6528 (mt) REVERT: V 21 ARG cc_start: 0.6171 (ttt90) cc_final: 0.5343 (mmt-90) REVERT: V 30 LYS cc_start: 0.7428 (ptmt) cc_final: 0.6910 (mmmt) REVERT: V 44 LYS cc_start: 0.6522 (mptm) cc_final: 0.6027 (mtpt) REVERT: W 45 ARG cc_start: 0.6915 (mtt180) cc_final: 0.6644 (mtm-85) REVERT: W 50 SER cc_start: 0.5821 (OUTLIER) cc_final: 0.5080 (p) REVERT: X 13 SER cc_start: 0.8631 (t) cc_final: 0.8217 (m) REVERT: X 24 GLN cc_start: 0.8150 (pt0) cc_final: 0.7918 (pt0) REVERT: X 87 GLU cc_start: 0.8350 (tp30) cc_final: 0.7880 (mm-30) REVERT: Y 37 LYS cc_start: 0.7167 (tptt) cc_final: 0.6645 (tmtt) REVERT: Y 95 GLU cc_start: 0.7910 (tt0) cc_final: 0.7564 (tt0) REVERT: Y 108 LYS cc_start: 0.8584 (mttt) cc_final: 0.7581 (mmtt) REVERT: Y 114 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: Y 139 GLU cc_start: 0.5642 (mm-30) cc_final: 0.4834 (mp0) REVERT: Y 140 ARG cc_start: 0.5702 (mtp-110) cc_final: 0.4703 (mtp180) REVERT: Z 8 ARG cc_start: 0.7355 (mtt-85) cc_final: 0.6047 (ttt90) REVERT: Z 15 ASN cc_start: 0.7357 (t0) cc_final: 0.6970 (t0) REVERT: Z 39 GLU cc_start: 0.7734 (mt-10) cc_final: 0.6974 (mp0) REVERT: Z 42 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7125 (pt0) REVERT: Z 47 MET cc_start: 0.6998 (ttp) cc_final: 0.6596 (ttp) REVERT: Z 48 TYR cc_start: 0.6587 (m-80) cc_final: 0.5792 (m-80) REVERT: Z 106 GLN cc_start: 0.7757 (mt0) cc_final: 0.7273 (mm110) REVERT: a 92 LEU cc_start: 0.7824 (tp) cc_final: 0.7539 (tp) REVERT: b 89 ARG cc_start: 0.6764 (mtp-110) cc_final: 0.6175 (mtt180) REVERT: b 94 ASP cc_start: 0.6739 (m-30) cc_final: 0.6472 (m-30) REVERT: c 26 GLN cc_start: 0.7318 (mt0) cc_final: 0.7049 (mt0) REVERT: c 36 LYS cc_start: 0.5488 (pttm) cc_final: 0.5118 (tptp) REVERT: c 72 ARG cc_start: 0.6376 (mtm180) cc_final: 0.6030 (ttm170) REVERT: d 54 ASP cc_start: 0.7484 (p0) cc_final: 0.7171 (p0) REVERT: d 57 THR cc_start: 0.7954 (m) cc_final: 0.7748 (m) REVERT: d 58 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6352 (mt) REVERT: e 8 TRP cc_start: 0.8204 (t-100) cc_final: 0.7467 (t-100) REVERT: e 13 LYS cc_start: 0.7902 (mttt) cc_final: 0.6908 (mmtm) REVERT: e 38 MET cc_start: 0.7632 (ttm) cc_final: 0.7284 (ttm) REVERT: f 96 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7705 (mm-30) REVERT: f 109 MET cc_start: 0.7904 (ttp) cc_final: 0.7694 (ttm) REVERT: f 126 LYS cc_start: 0.6235 (mtmt) cc_final: 0.5903 (pttt) REVERT: h 8 ARG cc_start: 0.5145 (ttt-90) cc_final: 0.4438 (tpt90) REVERT: h 15 ASN cc_start: 0.6905 (m-40) cc_final: 0.6559 (m-40) REVERT: h 30 MET cc_start: 0.4515 (tmm) cc_final: 0.3817 (mmt) REVERT: h 89 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6819 (tt) REVERT: h 113 PHE cc_start: 0.5503 (OUTLIER) cc_final: 0.4855 (m-80) REVERT: h 177 TRP cc_start: 0.6190 (m100) cc_final: 0.5703 (m100) REVERT: h 217 MET cc_start: 0.5464 (mtt) cc_final: 0.5042 (ttm) REVERT: h 235 ILE cc_start: 0.7476 (tt) cc_final: 0.7227 (tt) REVERT: h 264 LYS cc_start: 0.6328 (mptt) cc_final: 0.5587 (ttpt) REVERT: h 305 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6406 (m-40) REVERT: n 1 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6249 (tmm) REVERT: n 21 ARG cc_start: 0.6688 (ttt90) cc_final: 0.6267 (mtp180) outliers start: 178 outliers final: 134 residues processed: 964 average time/residue: 0.8460 time to fit residues: 1338.4098 Evaluate side-chains 975 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 822 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 32 MET Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 162 LEU Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 25 CYS Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 43 SER Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 93 SER Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 28 ASN Chi-restraints excluded: chain V residue 41 ARG Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain X residue 32 LYS Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 83 LEU Chi-restraints excluded: chain X residue 85 ASP Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 77 ASN Chi-restraints excluded: chain Y residue 81 ILE Chi-restraints excluded: chain Y residue 87 ASN Chi-restraints excluded: chain Y residue 97 ASN Chi-restraints excluded: chain Y residue 105 PHE Chi-restraints excluded: chain Y residue 114 ASP Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 6 THR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 120 THR Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 56 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain e residue 24 CYS Chi-restraints excluded: chain h residue 29 ASP Chi-restraints excluded: chain h residue 89 LEU Chi-restraints excluded: chain h residue 104 HIS Chi-restraints excluded: chain h residue 113 PHE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 168 CYS Chi-restraints excluded: chain h residue 248 LEU Chi-restraints excluded: chain h residue 258 ILE Chi-restraints excluded: chain h residue 289 LEU Chi-restraints excluded: chain h residue 305 ASN Chi-restraints excluded: chain n residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 0.8980 chunk 557 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 482 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 524 optimal weight: 0.6980 chunk 219 optimal weight: 7.9990 chunk 538 optimal weight: 0.1980 chunk 66 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN F 98 ASN J 84 ASN J 99 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN P 32 HIS ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 HIS ** b 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.172992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144044 restraints weight = 124435.295| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.02 r_work: 0.3556 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 84823 Z= 0.282 Angle : 0.731 59.188 123619 Z= 0.379 Chirality : 0.040 0.506 15363 Planarity : 0.006 0.114 8630 Dihedral : 23.931 179.794 35072 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 4.13 % Allowed : 23.00 % Favored : 72.88 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.12), residues: 4788 helix: 0.37 (0.13), residues: 1537 sheet: -1.19 (0.17), residues: 846 loop : -1.34 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP h 17 HIS 0.007 0.001 HIS L 66 PHE 0.026 0.002 PHE B 203 TYR 0.021 0.002 TYR L 12 ARG 0.007 0.001 ARG M 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22577.46 seconds wall clock time: 395 minutes 49.80 seconds (23749.80 seconds total)