Starting phenix.real_space_refine on Mon Feb 19 12:52:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/02_2024/6p4h_20249.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/02_2024/6p4h_20249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/02_2024/6p4h_20249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/02_2024/6p4h_20249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/02_2024/6p4h_20249.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4h_20249/02_2024/6p4h_20249.pdb" } resolution = 3.2 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 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "C ARG 51": "NH1" <-> "NH2" 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 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 ARG 166": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G ASP 27": "OD1" <-> "OD2" 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 ARG 198": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" 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 72": "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 "I PHE 192": "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 123": "NH1" <-> "NH2" Residue "J ARG 141": "NH1" <-> "NH2" Residue "J TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 114": "NH1" <-> "NH2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" 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 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 130": "NH1" <-> "NH2" Residue "R PHE 13": "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 "S ARG 5": "NH1" <-> "NH2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S PHE 128": "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 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 "X ARG 36": "NH1" <-> "NH2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 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 "f ARG 81": "NH1" <-> "NH2" Residue "f ARG 101": "NH1" <-> "NH2" Residue "f ARG 104": "NH1" <-> "NH2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 138": "NH1" <-> "NH2" 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: 0.09s 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': 144, 'rna2p_pyr': 109, 'rna3p_pur': 754, '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: "1" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 4323 Classifications: {'RNA': 203} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 17, 'rna3p_pur': 88, 'rna3p_pyr': 81} Link IDs: {'rna2p': 34, 'rna3p': 168} 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} Time building chain proxies: 29.79, per 1000 atoms: 0.38 Number of scatterers: 79374 At special positions: 0 Unit cell: (234.27, 261.396, 210.843, 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=5, symmetry=0 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=2.44 Simple disulfide: pdb=" SG CYS b 74 " - pdb=" SG CYS b 77 " distance=2.62 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 39 " distance=2.71 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 42 " distance=2.35 Simple disulfide: pdb=" SG CYS e 39 " - pdb=" SG CYS e 42 " distance=2.94 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: 29.25 Conformation dependent library (CDL) restraints added in 5.3 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: 155 helices and 56 sheets defined 35.0% alpha, 18.0% beta 526 base pairs and 1040 stacking pairs defined. Time for finding SS restraints: 24.25 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.739A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 38 removed outlier: 3.696A pdb=" N GLU B 35 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLN B 36 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 38 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.633A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 removed outlier: 4.162A pdb=" N ARG B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.854A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.649A pdb=" N GLY B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.595A pdb=" N TYR B 202 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.640A pdb=" N GLU B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.589A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 178 removed outlier: 4.314A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.604A pdb=" N ARG D 68 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 removed outlier: 3.961A pdb=" N PHE D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.663A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 removed outlier: 3.928A pdb=" N LEU D 102 " --> pdb=" O GLY D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.514A pdb=" N ALA D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.528A pdb=" N LYS D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 269 through 277 removed outlier: 4.038A pdb=" N MET D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 removed outlier: 3.547A pdb=" N VAL E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 60 removed outlier: 3.747A pdb=" N GLY E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.568A 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 111 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.744A pdb=" N VAL E 164 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 59 through 66 Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 247 through 263 Processing helix chain 'G' and resid 60 through 66 removed outlier: 4.154A pdb=" N LYS G 63 " --> pdb=" O ARG G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 77 removed outlier: 3.643A pdb=" N MET G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.506A pdb=" N GLY G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 163 Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'H' and resid 20 through 25 removed outlier: 3.640A pdb=" N LEU H 24 " --> pdb=" O ASP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 153 through 157 removed outlier: 3.887A pdb=" N VAL H 157 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 236 removed outlier: 4.601A pdb=" N LYS H 195 " --> pdb=" O ARG H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 33 Processing helix chain 'I' and resid 37 through 42 removed outlier: 4.689A pdb=" N GLU I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 74 removed outlier: 4.272A pdb=" N LYS I 70 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N SER I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS I 74 " --> pdb=" O LYS I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 85 removed outlier: 3.637A 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 134 removed outlier: 4.097A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 181 removed outlier: 4.122A pdb=" N GLY I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU I 180 " --> pdb=" O VAL I 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.756A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 117 Processing helix chain 'J' and resid 142 through 155 removed outlier: 3.700A pdb=" N GLN J 146 " --> pdb=" O SER J 142 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS J 147 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'J' and resid 192 through 207 Processing helix chain 'K' and resid 21 through 36 Processing helix chain 'K' and resid 39 through 62 removed outlier: 3.906A pdb=" N VAL K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL K 46 " --> pdb=" O GLU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 102 through 107 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 removed outlier: 3.649A pdb=" N ALA K 185 " --> pdb=" O GLY K 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.533A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.608A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 53 removed outlier: 3.864A pdb=" N ILE M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 28 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 90 removed outlier: 3.722A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'O' and resid 29 through 42 Processing helix chain 'O' and resid 46 through 58 removed outlier: 3.618A pdb=" N SER O 57 " --> pdb=" O ILE O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 70 through 79 removed outlier: 3.503A 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 64 through 68 removed outlier: 3.707A pdb=" N ASP P 67 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU P 68 " --> pdb=" O ASP P 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 64 through 68' Processing helix chain 'P' and resid 70 through 88 removed outlier: 3.692A pdb=" N LEU P 88 " --> pdb=" O ARG P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 122 Processing helix chain 'Q' and resid 22 through 27 Processing helix chain 'Q' and resid 29 through 35 removed outlier: 4.104A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 47 Processing helix chain 'Q' and resid 56 through 65 removed outlier: 3.502A pdb=" N LYS Q 62 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 90 Processing helix chain 'Q' and resid 108 through 112 removed outlier: 3.877A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 120 removed outlier: 4.014A pdb=" N PHE Q 119 " --> pdb=" O TYR Q 115 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER Q 120 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 115 through 120' Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 44 through 47 Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.620A pdb=" N LEU R 52 " --> pdb=" O GLN R 48 " (cutoff:3.500A) Proline residue: R 54 - end of helix removed outlier: 3.510A pdb=" N LEU R 58 " --> pdb=" O PRO R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.645A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.805A 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: 3.558A pdb=" N ALA S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 38 removed outlier: 3.859A pdb=" N ASN S 31 " --> pdb=" O ASP S 27 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG S 33 " --> pdb=" O HIS S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 64 removed outlier: 3.627A pdb=" N ARG S 47 " --> pdb=" O SER S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'S' and resid 99 through 108 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: 3.579A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 Processing helix chain 'T' and resid 74 through 78 Processing helix chain 'T' and resid 80 through 84 removed outlier: 3.514A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU T 84 " --> pdb=" O ASP T 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 80 through 84' Processing helix chain 'T' and resid 99 through 117 Processing helix chain 'T' and resid 119 through 127 Processing helix chain 'U' and resid 10 through 26 removed outlier: 3.575A pdb=" N PHE U 14 " --> pdb=" O ASN U 10 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL U 15 " --> pdb=" O GLN U 11 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.838A 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: 3.606A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 142 Processing helix chain 'V' and resid 29 through 45 Processing helix chain 'V' and resid 94 through 103 removed outlier: 3.694A pdb=" N SER V 103 " --> pdb=" O LYS V 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.602A 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: 4.000A pdb=" N VAL X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 93 removed outlier: 3.663A pdb=" N ASN X 92 " --> pdb=" O LYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 120 Processing helix chain 'Y' and resid 9 through 21 Processing helix chain 'Y' and resid 24 through 32 Processing helix chain 'Y' and resid 33 through 39 Processing helix chain 'Y' and resid 90 through 94 Processing helix chain 'Y' and resid 129 through 136 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.554A pdb=" N ILE Z 40 " --> pdb=" O PRO Z 36 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (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 85 removed outlier: 3.509A pdb=" N ALA Z 82 " --> pdb=" O SER Z 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 92 Processing helix chain 'Z' and resid 103 through 115 removed outlier: 3.752A pdb=" N ARG Z 107 " --> pdb=" O SER Z 103 " (cutoff:3.500A) Processing helix chain 'Z' and resid 118 through 123 removed outlier: 4.329A pdb=" N ALA Z 121 " --> pdb=" O ARG Z 118 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS Z 122 " --> pdb=" O GLY Z 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 62 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 Processing helix chain 'a' and resid 80 through 94 Processing helix chain 'b' and resid 49 through 57 removed outlier: 3.734A pdb=" N GLU b 55 " --> pdb=" O ARG b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'b' and resid 90 through 94 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.503A pdb=" N GLU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 36 Processing helix chain 'e' and resid 40 through 51 removed outlier: 5.926A pdb=" N LYS e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASP e 49 " --> pdb=" O GLN e 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 78 through 82 removed outlier: 3.854A pdb=" N VAL f 82 " --> pdb=" O LEU f 79 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 103 through 115 removed outlier: 3.823A pdb=" N ARG f 107 " --> pdb=" O GLY f 103 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 22 removed outlier: 3.504A pdb=" N GLN n 22 " --> pdb=" O ARG n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 23 through 25 No H-bonds generated for 'chain 'n' and resid 23 through 25' Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.713A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.101A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.306A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 128 removed outlier: 6.842A pdb=" N PHE C 138 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 120 through 128 removed outlier: 6.680A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 103 through 115 removed outlier: 5.803A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 188 Processing sheet with id=AA8, first strand: chain 'E' and resid 34 through 41 removed outlier: 3.694A pdb=" N ILE E 48 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AB1, first strand: chain 'E' and resid 209 through 210 removed outlier: 3.719A pdb=" N SER E 209 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 10 removed outlier: 4.335A pdb=" N LEU F 9 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'F' and resid 70 through 72 removed outlier: 4.194A pdb=" N HIS F 112 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 137 through 141 removed outlier: 6.491A pdb=" N HIS F 138 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE F 129 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL F 140 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR F 159 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE F 172 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN F 161 " --> pdb=" O THR F 170 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS F 168 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 207 through 211 removed outlier: 7.252A pdb=" N VAL F 207 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ARG F 198 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N HIS F 209 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU F 180 " --> pdb=" O ILE F 228 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 123 through 125 removed outlier: 8.611A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS d 27 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG d 20 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN d 29 " --> pdb=" O LEU d 18 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU d 33 " --> pdb=" O VAL d 14 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL d 14 " --> pdb=" O GLU d 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.799A pdb=" N LYS H 2 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU H 111 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASN H 4 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE H 113 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER H 6 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N LYS H 115 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 72 through 77 Processing sheet with id=AC1, first strand: chain 'H' and resid 160 through 161 Processing sheet with id=AC2, first strand: chain 'I' and resid 48 through 53 removed outlier: 3.689A pdb=" N VAL I 53 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE I 95 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 185 through 188 removed outlier: 5.832A pdb=" N LEU I 153 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE I 144 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS I 155 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS I 142 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N HIS I 157 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.587A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN J 52 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 62 through 67 removed outlier: 7.191A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP J 80 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE J 101 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AC7, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AC8, first strand: chain 'M' and resid 72 through 79 removed outlier: 16.728A pdb=" N LEU M 73 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 15.512A pdb=" N LEU M 93 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY M 75 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASP M 91 " --> pdb=" O GLY M 75 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL M 77 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG M 89 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 77 through 78 removed outlier: 3.620A pdb=" N LEU N 49 " --> pdb=" O VAL N 111 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 52 through 57 removed outlier: 3.534A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 16 through 17 Processing sheet with id=AD3, first strand: chain 'Q' and resid 76 through 78 Processing sheet with id=AD4, first strand: chain 'R' and resid 10 through 15 Processing sheet with id=AD5, first strand: chain 'S' and resid 96 through 98 removed outlier: 6.335A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'T' and resid 12 through 14 Processing sheet with id=AD7, first strand: chain 'U' and resid 81 through 83 Processing sheet with id=AD8, first strand: chain 'U' and resid 114 through 115 Processing sheet with id=AD9, first strand: chain 'V' and resid 50 through 55 removed outlier: 6.592A pdb=" N VAL V 50 " --> pdb=" O HIS V 92 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS V 92 " --> pdb=" O VAL V 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY V 52 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP V 90 " --> pdb=" O GLY V 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 50 through 55 removed outlier: 6.592A pdb=" N VAL V 50 " --> pdb=" O HIS V 92 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS V 92 " --> pdb=" O VAL V 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY V 52 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP V 90 " --> pdb=" O GLY V 52 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 32 through 39 removed outlier: 3.710A pdb=" N GLU W 38 " --> pdb=" O GLN W 49 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 71 through 74 Processing sheet with id=AE4, first strand: chain 'X' and resid 71 through 74 removed outlier: 5.314A pdb=" N ILE X 125 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N THR X 105 " --> pdb=" O ILE X 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 46 through 58 removed outlier: 7.299A pdb=" N ARG Y 71 " --> pdb=" O LEU Y 52 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS Y 54 " --> pdb=" O CYS Y 69 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS Y 69 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY Y 56 " --> pdb=" O ARG Y 67 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG Y 67 " --> pdb=" O GLY Y 56 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE Y 120 " --> pdb=" O THR Y 82 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.735A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'a' and resid 97 through 101 removed outlier: 7.004A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AE9, first strand: chain 'b' and resid 36 through 40 Processing sheet with id=AF1, first strand: chain 'c' and resid 44 through 47 Processing sheet with id=AF2, first strand: chain 'c' and resid 54 through 55 removed outlier: 6.777A pdb=" N VAL c 54 " --> pdb=" O LEU c 63 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.623A pdb=" N MET e 38 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 133 through 134 removed outlier: 3.521A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'h' and resid 10 through 11 Processing sheet with id=AF6, first strand: chain 'h' and resid 21 through 22 removed outlier: 5.793A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.616A pdb=" N SER h 82 " --> pdb=" O THR h 86 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR h 86 " --> pdb=" O SER h 82 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU h 87 " --> pdb=" O ARG h 100 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG h 100 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU h 89 " --> pdb=" O THR h 98 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR h 96 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 108 through 113 removed outlier: 3.826A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 153 through 156 removed outlier: 3.770A pdb=" N CYS h 153 " --> pdb=" O CYS h 168 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 195 through 200 removed outlier: 3.520A pdb=" N GLY h 210 " --> pdb=" O THR h 197 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY h 211 " --> pdb=" O GLN h 215 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN h 215 " --> pdb=" O GLY h 211 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR h 228 " --> pdb=" O LEU h 218 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP h 220 " --> pdb=" O HIS h 226 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N HIS h 226 " --> pdb=" O ASP h 220 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.105A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE h 256 " --> pdb=" O GLU h 269 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU h 269 " --> pdb=" O ILE h 256 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE h 258 " --> pdb=" O VAL h 267 " (cutoff:3.500A) 1477 hydrogen bonds defined for protein. 4191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1320 hydrogen bonds 2132 hydrogen bond angles 0 basepair planarities 526 basepair parallelities 1040 stacking parallelities Total time for adding SS restraints: 64.95 Time building geometry restraints manager: 31.94 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: 10963 1.33 - 1.45: 32305 1.45 - 1.58: 37498 1.58 - 1.70: 3777 1.70 - 1.82: 280 Bond restraints: 84823 Sorted by residual: bond pdb=" O3' U 2 885 " pdb=" P A 2 886 " ideal model delta sigma weight residual 1.607 1.677 -0.070 1.50e-02 4.44e+03 2.20e+01 bond pdb=" N VAL H 129 " pdb=" CA VAL H 129 " ideal model delta sigma weight residual 1.456 1.495 -0.039 8.70e-03 1.32e+04 1.98e+01 bond pdb=" N ILE P 135 " pdb=" CA ILE P 135 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.30e-03 1.88e+04 1.88e+01 bond pdb=" N ILE K 144 " pdb=" CA ILE K 144 " ideal model delta sigma weight residual 1.456 1.494 -0.037 8.70e-03 1.32e+04 1.83e+01 bond pdb=" N VAL I 166 " pdb=" CA VAL I 166 " ideal model delta sigma weight residual 1.459 1.496 -0.038 9.10e-03 1.21e+04 1.73e+01 ... (remaining 84818 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.75: 10072 105.75 - 113.01: 45714 113.01 - 120.28: 38748 120.28 - 127.54: 25632 127.54 - 134.81: 3453 Bond angle restraints: 123619 Sorted by residual: angle pdb=" O3' U 16506 " pdb=" C3' U 16506 " pdb=" C2' U 16506 " ideal model delta sigma weight residual 109.50 125.20 -15.70 1.50e+00 4.44e-01 1.10e+02 angle pdb=" C4' A 21664 " pdb=" C3' A 21664 " pdb=" O3' A 21664 " ideal model delta sigma weight residual 109.40 124.67 -15.27 1.50e+00 4.44e-01 1.04e+02 angle pdb=" O3' A 21489 " pdb=" C3' A 21489 " pdb=" C2' A 21489 " ideal model delta sigma weight residual 109.50 122.88 -13.38 1.50e+00 4.44e-01 7.96e+01 angle pdb=" O3' U 2 688 " pdb=" C3' U 2 688 " pdb=" C2' U 2 688 " ideal model delta sigma weight residual 109.50 122.80 -13.30 1.50e+00 4.44e-01 7.86e+01 angle pdb=" C4' A 2 870 " pdb=" C3' A 2 870 " pdb=" O3' A 2 870 " ideal model delta sigma weight residual 109.40 121.22 -11.82 1.50e+00 4.44e-01 6.21e+01 ... (remaining 123614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 48715 35.91 - 71.82: 4718 71.82 - 107.72: 610 107.72 - 143.63: 21 143.63 - 179.54: 57 Dihedral angle restraints: 54121 sinusoidal: 40144 harmonic: 13977 Sorted by residual: dihedral pdb=" CA LYS G 18 " pdb=" C LYS G 18 " pdb=" N LEU G 19 " pdb=" CA LEU G 19 " ideal model delta harmonic sigma weight residual -180.00 -111.64 -68.36 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CA GLN Y 61 " pdb=" C GLN Y 61 " pdb=" N PRO Y 62 " pdb=" CA PRO Y 62 " ideal model delta harmonic sigma weight residual -180.00 -127.25 -52.75 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" C5' U 16456 " pdb=" C4' U 16456 " pdb=" C3' U 16456 " pdb=" O3' U 16456 " ideal model delta sinusoidal sigma weight residual 147.00 77.45 69.55 1 8.00e+00 1.56e-02 9.76e+01 ... (remaining 54118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 12254 0.127 - 0.255: 3028 0.255 - 0.382: 64 0.382 - 0.510: 10 0.510 - 0.637: 7 Chirality restraints: 15363 Sorted by residual: 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 -2.11 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C3' A 21637 " pdb=" C4' A 21637 " pdb=" O3' A 21637 " pdb=" C2' A 21637 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.59 2.00e-01 2.50e+01 8.70e+00 chirality pdb=" C3' U 2 553 " pdb=" C4' U 2 553 " pdb=" O3' U 2 553 " pdb=" C2' U 2 553 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.58 2.00e-01 2.50e+01 8.48e+00 ... (remaining 15360 not shown) Planarity restraints: 8630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO Q 125 " 0.022 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C PRO Q 125 " -0.080 2.00e-02 2.50e+03 pdb=" O PRO Q 125 " 0.031 2.00e-02 2.50e+03 pdb=" N VAL Q 126 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 662 " -0.052 2.00e-02 2.50e+03 2.28e-02 1.56e+01 pdb=" N9 G 2 662 " 0.050 2.00e-02 2.50e+03 pdb=" C8 G 2 662 " 0.015 2.00e-02 2.50e+03 pdb=" N7 G 2 662 " 0.009 2.00e-02 2.50e+03 pdb=" C5 G 2 662 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G 2 662 " -0.016 2.00e-02 2.50e+03 pdb=" O6 G 2 662 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G 2 662 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G 2 662 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G 2 662 " 0.014 2.00e-02 2.50e+03 pdb=" N3 G 2 662 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G 2 662 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN Y 61 " 0.016 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C GLN Y 61 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN Y 61 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO Y 62 " 0.018 2.00e-02 2.50e+03 ... (remaining 8627 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 6310 2.72 - 3.27: 69137 3.27 - 3.81: 149700 3.81 - 4.36: 196032 4.36 - 4.90: 272585 Nonbonded interactions: 693764 Sorted by model distance: nonbonded pdb=" O2' A 21291 " pdb=" OH TYR g 140 " model vdw 2.179 2.440 nonbonded pdb=" OP1 C 21568 " pdb=" OG SER U 96 " model vdw 2.199 2.440 nonbonded pdb=" O2' A 16457 " pdb=" O4' A 16458 " model vdw 2.203 2.440 nonbonded pdb=" O2' G 2 146 " pdb=" O5' A 2 147 " model vdw 2.226 2.440 nonbonded pdb=" O2' U 21535 " pdb=" OD1 ASN G 82 " model vdw 2.239 2.440 ... (remaining 693759 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: 2.360 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: 0.060 Extract box with map and model: 9.170 Check model and map are aligned: 0.850 Set scattering table: 0.530 Process input model: 206.920 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.220 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 224.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 0.070 84823 Z= 0.642 Angle : 1.433 15.698 123619 Z= 1.017 Chirality : 0.099 0.637 15363 Planarity : 0.004 0.046 8630 Dihedral : 22.889 179.540 45088 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.56 % Favored : 92.77 % Rotamer: Outliers : 2.17 % Allowed : 6.32 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.35 % 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: -3.62 (0.10), residues: 4788 helix: -2.51 (0.10), residues: 1497 sheet: -2.53 (0.16), residues: 787 loop : -2.24 (0.11), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP T 82 HIS 0.012 0.002 HIS M 94 PHE 0.026 0.003 PHE h 113 TYR 0.031 0.003 TYR O 141 ARG 0.008 0.001 ARG X 28 *********************** 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 1629 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1538 time to evaluate : 4.285 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: B 12 GLU cc_start: 0.7242 (tm-30) cc_final: 0.6997 (tm-30) REVERT: B 40 LYS cc_start: 0.7639 (tttm) cc_final: 0.7216 (tttt) REVERT: B 52 LYS cc_start: 0.7906 (tttt) cc_final: 0.7577 (ttpt) REVERT: B 69 GLU cc_start: 0.7674 (tt0) cc_final: 0.7154 (tp30) REVERT: B 75 SER cc_start: 0.9071 (t) cc_final: 0.8633 (m) REVERT: B 78 SER cc_start: 0.9171 (t) cc_final: 0.8928 (t) REVERT: B 80 ARG cc_start: 0.7031 (mtp-110) cc_final: 0.6690 (mtm180) REVERT: B 109 THR cc_start: 0.8579 (m) cc_final: 0.7939 (p) REVERT: B 112 ILE cc_start: 0.8103 (mt) cc_final: 0.7725 (tt) REVERT: B 126 ASP cc_start: 0.8073 (t0) cc_final: 0.7428 (t0) REVERT: B 136 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: B 138 SER cc_start: 0.8226 (t) cc_final: 0.7963 (p) REVERT: B 145 ILE cc_start: 0.8444 (mt) cc_final: 0.8216 (mt) REVERT: B 177 MET cc_start: 0.8248 (mmt) cc_final: 0.7923 (tpt) REVERT: B 181 GLU cc_start: 0.7291 (tp30) cc_final: 0.6909 (tp30) REVERT: B 185 MET cc_start: 0.8064 (mtp) cc_final: 0.7514 (mtt) REVERT: B 192 GLU cc_start: 0.6361 (mm-30) cc_final: 0.5486 (mp0) REVERT: B 209 GLU cc_start: 0.4933 (mt-10) cc_final: 0.4360 (tp30) REVERT: C 56 LYS cc_start: 0.7033 (pttt) cc_final: 0.6494 (mmmt) REVERT: C 75 GLN cc_start: 0.6992 (tp40) cc_final: 0.6585 (mm-40) REVERT: C 83 LYS cc_start: 0.7525 (mtmt) cc_final: 0.6903 (mttt) REVERT: C 85 LYS cc_start: 0.7868 (mttt) cc_final: 0.7618 (mtmt) REVERT: C 89 GLU cc_start: 0.8039 (tt0) cc_final: 0.7280 (mm-30) REVERT: C 107 ARG cc_start: 0.7761 (ptp-110) cc_final: 0.7155 (ptp-170) REVERT: C 108 ASP cc_start: 0.7879 (t0) cc_final: 0.7533 (t70) REVERT: C 118 GLN cc_start: 0.8738 (pt0) cc_final: 0.8350 (pt0) REVERT: C 122 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8105 (mt-10) REVERT: C 144 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7423 (tttp) REVERT: C 149 GLN cc_start: 0.8315 (tt0) cc_final: 0.8082 (tt0) REVERT: C 169 MET cc_start: 0.8448 (mtt) cc_final: 0.8022 (mtm) REVERT: C 182 LYS cc_start: 0.7084 (tmtt) cc_final: 0.6806 (mtmt) REVERT: C 193 ILE cc_start: 0.6504 (mt) cc_final: 0.6213 (tt) REVERT: C 207 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7749 (pp) REVERT: C 229 MET cc_start: 0.6669 (mmt) cc_final: 0.6387 (mmt) REVERT: D 73 MET cc_start: 0.7302 (mpt) cc_final: 0.6786 (mmm) REVERT: D 79 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7664 (mm-30) REVERT: D 80 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7657 (mt-10) REVERT: D 92 GLU cc_start: 0.7771 (mp0) cc_final: 0.7515 (mp0) REVERT: D 103 LYS cc_start: 0.7625 (mttt) cc_final: 0.7383 (mttp) REVERT: D 105 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7193 (mt-10) REVERT: D 117 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7104 (ttm-80) REVERT: D 144 SER cc_start: 0.8155 (t) cc_final: 0.7703 (m) REVERT: D 146 GLU cc_start: 0.8000 (pm20) cc_final: 0.7603 (mp0) REVERT: D 152 ARG cc_start: 0.7660 (ttm110) cc_final: 0.7357 (ttp-110) REVERT: D 161 SER cc_start: 0.9066 (t) cc_final: 0.8771 (p) REVERT: D 176 LYS cc_start: 0.7672 (mttm) cc_final: 0.7456 (mmtp) REVERT: E 1 MET cc_start: 0.5353 (ttt) cc_final: 0.4449 (ptp) REVERT: E 5 ILE cc_start: 0.7165 (pt) cc_final: 0.6938 (tt) REVERT: E 14 ASP cc_start: 0.7971 (t0) cc_final: 0.7612 (t0) REVERT: E 31 GLU cc_start: 0.7265 (pm20) cc_final: 0.6813 (pm20) REVERT: E 46 THR cc_start: 0.6335 (m) cc_final: 0.5336 (p) REVERT: E 54 ARG cc_start: 0.5157 (mtm-85) cc_final: 0.4846 (mtt90) REVERT: E 61 GLU cc_start: 0.8085 (tt0) cc_final: 0.7877 (mt-10) REVERT: E 67 ARG cc_start: 0.7066 (mtm-85) cc_final: 0.6860 (mtm-85) REVERT: E 84 VAL cc_start: 0.7722 (p) cc_final: 0.7398 (p) REVERT: E 85 GLU cc_start: 0.7359 (pt0) cc_final: 0.6560 (tm-30) REVERT: E 87 TYR cc_start: 0.6636 (m-80) cc_final: 0.5838 (m-80) REVERT: E 89 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6609 (tt0) REVERT: E 113 LEU cc_start: 0.7097 (tp) cc_final: 0.6666 (tp) REVERT: E 117 ARG cc_start: 0.7375 (tpt-90) cc_final: 0.6575 (ttm110) REVERT: E 120 TYR cc_start: 0.8082 (m-80) cc_final: 0.6548 (t80) REVERT: E 124 ARG cc_start: 0.8121 (tpt170) cc_final: 0.7856 (ttt-90) REVERT: E 125 PHE cc_start: 0.6967 (t80) cc_final: 0.6694 (t80) REVERT: E 146 ARG cc_start: 0.7499 (tpp80) cc_final: 0.5982 (ptm160) REVERT: E 162 ASP cc_start: 0.8398 (t70) cc_final: 0.8165 (t0) REVERT: F 7 LYS cc_start: 0.8070 (mttt) cc_final: 0.7725 (mtmt) REVERT: F 32 SER cc_start: 0.8719 (t) cc_final: 0.8498 (p) REVERT: F 39 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7495 (mtp-110) REVERT: F 47 PHE cc_start: 0.8585 (t80) cc_final: 0.8179 (t80) REVERT: F 49 ARG cc_start: 0.7662 (ptt90) cc_final: 0.7379 (ttp-170) REVERT: F 71 LYS cc_start: 0.7519 (tttt) cc_final: 0.7051 (ttmt) REVERT: F 79 ASP cc_start: 0.7611 (t0) cc_final: 0.7288 (t0) REVERT: F 116 PRO cc_start: 0.7839 (Cg_exo) cc_final: 0.7497 (Cg_endo) REVERT: F 120 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7596 (mtpp) REVERT: F 143 ASP cc_start: 0.8400 (p0) cc_final: 0.8022 (p0) REVERT: F 155 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6601 (mmtt) REVERT: F 163 ASP cc_start: 0.7137 (t0) cc_final: 0.6687 (t0) REVERT: F 164 LEU cc_start: 0.7192 (mp) cc_final: 0.6707 (mt) REVERT: F 165 GLU cc_start: 0.6462 (pt0) cc_final: 0.6191 (mp0) REVERT: F 173 ILE cc_start: 0.8413 (mp) cc_final: 0.8186 (mp) REVERT: F 176 ASP cc_start: 0.6625 (m-30) cc_final: 0.6400 (t0) REVERT: F 205 PHE cc_start: 0.7163 (m-80) cc_final: 0.6797 (m-10) REVERT: F 212 ASP cc_start: 0.6787 (t70) cc_final: 0.6528 (t70) REVERT: F 221 ARG cc_start: 0.7667 (ttm170) cc_final: 0.7266 (mtt180) REVERT: F 232 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7769 (t0) REVERT: F 255 ARG cc_start: 0.7306 (ttp80) cc_final: 0.6973 (ptm-80) REVERT: G 20 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7259 (t80) REVERT: G 37 ASP cc_start: 0.8278 (t70) cc_final: 0.7952 (m-30) REVERT: G 42 LYS cc_start: 0.7785 (tttt) cc_final: 0.7569 (mtpt) REVERT: G 43 GLU cc_start: 0.7866 (tp30) cc_final: 0.7658 (tm-30) REVERT: G 44 LYS cc_start: 0.7735 (tttt) cc_final: 0.6938 (mmtt) REVERT: G 59 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7907 (tppt) REVERT: G 77 MET cc_start: 0.9317 (ptt) cc_final: 0.9026 (ptt) REVERT: G 94 LYS cc_start: 0.6876 (tttt) cc_final: 0.6564 (ttpp) REVERT: G 160 GLU cc_start: 0.7684 (tt0) cc_final: 0.7307 (tt0) REVERT: G 191 LYS cc_start: 0.7217 (tttt) cc_final: 0.6765 (ttmt) REVERT: H 17 GLU cc_start: 0.7237 (pt0) cc_final: 0.6559 (tt0) REVERT: H 24 LEU cc_start: 0.5769 (mt) cc_final: 0.5555 (mt) REVERT: H 29 GLU cc_start: 0.7892 (tt0) cc_final: 0.7655 (mm-30) REVERT: H 44 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7057 (tp30) REVERT: H 84 TYR cc_start: 0.7746 (t80) cc_final: 0.7467 (t80) REVERT: H 89 THR cc_start: 0.8585 (m) cc_final: 0.8300 (p) REVERT: H 95 LYS cc_start: 0.6985 (mmpt) cc_final: 0.6257 (mtpt) REVERT: H 121 ILE cc_start: 0.5769 (tp) cc_final: 0.5406 (mt) REVERT: H 131 ARG cc_start: 0.5173 (mpt90) cc_final: 0.4853 (mtm110) REVERT: H 154 ARG cc_start: 0.6772 (mpt-90) cc_final: 0.6509 (mpp80) REVERT: H 200 LYS cc_start: 0.6980 (tttt) cc_final: 0.6358 (mmtp) REVERT: H 203 LYS cc_start: 0.7787 (tttt) cc_final: 0.7083 (ptmt) REVERT: H 213 LEU cc_start: 0.7703 (tm) cc_final: 0.7503 (tp) REVERT: H 217 MET cc_start: 0.6583 (tpp) cc_final: 0.5879 (mmp) REVERT: H 219 GLU cc_start: 0.6122 (mt-10) cc_final: 0.5338 (mm-30) REVERT: I 15 LYS cc_start: 0.6613 (mttm) cc_final: 0.6363 (mptt) REVERT: I 40 LEU cc_start: 0.6743 (mt) cc_final: 0.6442 (mt) REVERT: I 53 VAL cc_start: 0.5675 (p) cc_final: 0.4752 (m) REVERT: I 99 ARG cc_start: 0.6675 (ttt180) cc_final: 0.6259 (mmm160) REVERT: I 105 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.7259 (t) REVERT: I 107 LYS cc_start: 0.5321 (mttt) cc_final: 0.5064 (pttt) REVERT: I 155 LYS cc_start: 0.6547 (mttt) cc_final: 0.6305 (mtmt) REVERT: I 162 GLN cc_start: 0.6807 (mp-120) cc_final: 0.6418 (mp10) REVERT: I 163 GLN cc_start: 0.6686 (tt0) cc_final: 0.5999 (tm-30) REVERT: I 191 GLU cc_start: 0.5486 (pm20) cc_final: 0.4640 (mt-10) REVERT: J 53 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7989 (mtmm) REVERT: J 83 TYR cc_start: 0.7838 (t80) cc_final: 0.7565 (t80) REVERT: J 84 ASN cc_start: 0.8029 (t0) cc_final: 0.7254 (t0) REVERT: J 91 VAL cc_start: 0.7364 (t) cc_final: 0.6898 (t) REVERT: J 92 ARG cc_start: 0.7683 (ttp-170) cc_final: 0.6536 (ttp80) REVERT: J 94 LYS cc_start: 0.7890 (mttt) cc_final: 0.7578 (mmmt) REVERT: J 95 THR cc_start: 0.8389 (m) cc_final: 0.8011 (p) REVERT: J 113 TYR cc_start: 0.7871 (t80) cc_final: 0.7652 (t80) REVERT: J 144 LYS cc_start: 0.7073 (ptpt) cc_final: 0.6212 (mmtt) REVERT: J 151 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6745 (pp20) REVERT: J 157 LYS cc_start: 0.7147 (tttt) cc_final: 0.6713 (mmtm) REVERT: J 163 GLU cc_start: 0.7561 (tt0) cc_final: 0.7260 (tm-30) REVERT: J 200 ARG cc_start: 0.8184 (ttp-170) cc_final: 0.7746 (ttm-80) REVERT: K 17 ARG cc_start: 0.7884 (ttt90) cc_final: 0.6915 (ttm-80) REVERT: K 18 ARG cc_start: 0.8337 (mtt90) cc_final: 0.7727 (mmt180) REVERT: K 21 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7290 (mm-30) REVERT: K 53 ILE cc_start: 0.8015 (mt) cc_final: 0.7746 (mt) REVERT: K 101 LYS cc_start: 0.7962 (ptmt) cc_final: 0.6917 (mmtm) REVERT: K 138 ARG cc_start: 0.7360 (mtt180) cc_final: 0.6715 (mtt-85) REVERT: K 154 GLN cc_start: 0.7617 (tt0) cc_final: 0.7356 (tt0) REVERT: L 8 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.7034 (ttm170) REVERT: L 9 ILE cc_start: 0.7833 (mt) cc_final: 0.7445 (pt) REVERT: L 16 PHE cc_start: 0.7058 (t80) cc_final: 0.6843 (t80) REVERT: L 26 ASP cc_start: 0.8379 (t0) cc_final: 0.7657 (t0) REVERT: L 52 LEU cc_start: 0.7454 (mm) cc_final: 0.7198 (mm) REVERT: L 53 LYS cc_start: 0.7242 (ttpp) cc_final: 0.6980 (tmtt) REVERT: M 37 TYR cc_start: 0.8009 (p90) cc_final: 0.7550 (p90) REVERT: M 45 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7746 (mtpt) REVERT: M 97 ARG cc_start: 0.7438 (ptt90) cc_final: 0.6964 (ttt90) REVERT: M 109 MET cc_start: 0.8645 (ptp) cc_final: 0.8178 (ptp) REVERT: M 111 VAL cc_start: 0.8298 (t) cc_final: 0.8053 (m) REVERT: M 140 PHE cc_start: 0.8328 (m-80) cc_final: 0.8116 (m-80) REVERT: N 102 LYS cc_start: 0.4553 (ttpt) cc_final: 0.3907 (mmmt) REVERT: N 112 LYS cc_start: 0.5999 (tmtt) cc_final: 0.4667 (ptpt) REVERT: O 27 LYS cc_start: 0.6656 (OUTLIER) cc_final: 0.5755 (mmtp) REVERT: O 29 THR cc_start: 0.7939 (p) cc_final: 0.7636 (p) REVERT: O 42 LYS cc_start: 0.7018 (ttmp) cc_final: 0.6805 (mtmm) REVERT: O 75 LEU cc_start: 0.7159 (mp) cc_final: 0.6762 (mp) REVERT: O 89 TYR cc_start: 0.7479 (t80) cc_final: 0.7275 (t80) REVERT: O 106 ARG cc_start: 0.7819 (mmt90) cc_final: 0.7057 (ttp80) REVERT: O 107 LYS cc_start: 0.7304 (tppp) cc_final: 0.6548 (mptt) REVERT: O 140 LYS cc_start: 0.7663 (ttmm) cc_final: 0.7428 (tppt) REVERT: P 54 CYS cc_start: 0.7934 (t) cc_final: 0.7473 (p) REVERT: P 63 LYS cc_start: 0.8384 (mmtp) cc_final: 0.7830 (ptpp) REVERT: P 75 MET cc_start: 0.7323 (ttp) cc_final: 0.6645 (tmm) REVERT: P 81 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7048 (t) REVERT: P 107 THR cc_start: 0.8130 (m) cc_final: 0.7598 (t) REVERT: P 113 GLN cc_start: 0.7304 (mt0) cc_final: 0.6656 (tt0) REVERT: P 143 LYS cc_start: 0.8224 (tmmt) cc_final: 0.7335 (tttp) REVERT: Q 22 LEU cc_start: 0.7610 (tp) cc_final: 0.7347 (tp) REVERT: Q 34 MET cc_start: 0.7808 (mtt) cc_final: 0.7076 (mtp) REVERT: Q 35 GLN cc_start: 0.8639 (mt0) cc_final: 0.7748 (mm-40) REVERT: Q 86 LEU cc_start: 0.7725 (mt) cc_final: 0.7367 (mp) REVERT: Q 92 SER cc_start: 0.8291 (t) cc_final: 0.8071 (t) REVERT: Q 101 THR cc_start: 0.7828 (m) cc_final: 0.7344 (p) REVERT: Q 108 LYS cc_start: 0.7654 (ptpt) cc_final: 0.6952 (mmpt) REVERT: Q 111 MET cc_start: 0.7215 (mmt) cc_final: 0.7005 (mmt) REVERT: R 43 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7345 (mm-30) REVERT: R 108 ILE cc_start: 0.7000 (mt) cc_final: 0.6671 (pt) REVERT: R 109 LYS cc_start: 0.7344 (ttmm) cc_final: 0.7033 (tttt) REVERT: R 116 ASP cc_start: 0.7075 (t70) cc_final: 0.6750 (t70) REVERT: R 128 GLU cc_start: 0.8630 (tt0) cc_final: 0.8338 (tt0) REVERT: S 27 ASP cc_start: 0.8271 (t70) cc_final: 0.7952 (t0) REVERT: S 62 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7529 (mt0) REVERT: S 80 ARG cc_start: 0.6929 (tmm160) cc_final: 0.6573 (ttp-110) REVERT: S 81 ARG cc_start: 0.6905 (tmm-80) cc_final: 0.6426 (ttp-170) REVERT: S 97 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7125 (mm-30) REVERT: S 121 GLN cc_start: 0.5238 (pp30) cc_final: 0.4876 (pm20) REVERT: S 126 MET cc_start: 0.5849 (ttp) cc_final: 0.5617 (ptm) REVERT: S 127 ASN cc_start: 0.7088 (t160) cc_final: 0.6880 (p0) REVERT: T 4 VAL cc_start: 0.6318 (m) cc_final: 0.5928 (t) REVERT: T 10 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6557 (mm-40) REVERT: T 19 ASN cc_start: 0.7560 (m110) cc_final: 0.7098 (m-40) REVERT: T 21 ASP cc_start: 0.8157 (t0) cc_final: 0.7768 (t0) REVERT: T 24 ARG cc_start: 0.7002 (mtp85) cc_final: 0.6617 (mtm-85) REVERT: T 46 ARG cc_start: 0.6705 (tpp-160) cc_final: 0.5828 (tpt90) REVERT: T 63 GLU cc_start: 0.7286 (tt0) cc_final: 0.6721 (tp30) REVERT: T 66 ARG cc_start: 0.6858 (ttm170) cc_final: 0.6656 (ttt90) REVERT: T 78 LYS cc_start: 0.7532 (ttmt) cc_final: 0.6932 (tptt) REVERT: T 94 LYS cc_start: 0.8206 (mttt) cc_final: 0.7900 (mttp) REVERT: T 106 LYS cc_start: 0.6234 (mmtt) cc_final: 0.6025 (mmtp) REVERT: T 112 GLU cc_start: 0.7789 (tt0) cc_final: 0.6786 (tm-30) REVERT: T 134 GLN cc_start: 0.8791 (mp10) cc_final: 0.8067 (mp10) REVERT: T 142 ARG cc_start: 0.5403 (OUTLIER) cc_final: 0.4421 (pmt-80) REVERT: U 27 LYS cc_start: 0.7492 (ptpp) cc_final: 0.7213 (ptmt) REVERT: U 35 ASP cc_start: 0.7614 (m-30) cc_final: 0.7394 (m-30) REVERT: U 114 GLU cc_start: 0.7442 (tt0) cc_final: 0.7231 (tm-30) REVERT: U 134 ILE cc_start: 0.7790 (pt) cc_final: 0.7303 (mt) REVERT: U 137 GLN cc_start: 0.7799 (mt0) cc_final: 0.7522 (mt0) REVERT: V 23 THR cc_start: 0.7744 (m) cc_final: 0.7461 (p) REVERT: V 47 ASN cc_start: 0.6932 (t160) cc_final: 0.6374 (m-40) REVERT: V 55 ARG cc_start: 0.7185 (mpt180) cc_final: 0.6608 (mtt90) REVERT: W 1 MET cc_start: 0.6689 (mpp) cc_final: 0.6045 (tpt) REVERT: W 11 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6984 (pp) REVERT: W 15 ARG cc_start: 0.8338 (mtm180) cc_final: 0.8047 (mtp180) REVERT: W 21 ASN cc_start: 0.8075 (t0) cc_final: 0.7062 (t0) REVERT: W 34 MET cc_start: 0.6684 (ttp) cc_final: 0.6281 (ttm) REVERT: W 38 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6113 (mt-10) REVERT: W 41 LYS cc_start: 0.7591 (pttt) cc_final: 0.7358 (ptpp) REVERT: W 45 ARG cc_start: 0.7522 (mtt180) cc_final: 0.7217 (mtt180) REVERT: X 14 ILE cc_start: 0.8394 (pt) cc_final: 0.8015 (pt) REVERT: X 33 VAL cc_start: 0.8519 (t) cc_final: 0.8148 (p) REVERT: X 43 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7883 (mmmm) REVERT: X 86 LEU cc_start: 0.7888 (tp) cc_final: 0.7633 (tt) REVERT: X 87 GLU cc_start: 0.7743 (tp30) cc_final: 0.7485 (mm-30) REVERT: X 91 ASN cc_start: 0.8341 (t0) cc_final: 0.7753 (m-40) REVERT: X 104 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8062 (pp) REVERT: X 111 MET cc_start: 0.8625 (ptt) cc_final: 0.8202 (ptt) REVERT: X 117 ARG cc_start: 0.6789 (tpp80) cc_final: 0.6327 (mtt-85) REVERT: X 130 PHE cc_start: 0.8590 (p90) cc_final: 0.7755 (p90) REVERT: Y 11 ARG cc_start: 0.8677 (ptp-110) cc_final: 0.8436 (ttm110) REVERT: Y 15 SER cc_start: 0.8792 (p) cc_final: 0.8379 (m) REVERT: Y 37 LYS cc_start: 0.6791 (tptt) cc_final: 0.6423 (mmmt) REVERT: Y 80 LYS cc_start: 0.7936 (mttt) cc_final: 0.7711 (mmtt) REVERT: Y 107 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8080 (mtp180) REVERT: Y 108 LYS cc_start: 0.7727 (mttt) cc_final: 0.7353 (mptt) REVERT: Y 125 VAL cc_start: 0.8224 (t) cc_final: 0.7948 (p) REVERT: Y 135 LYS cc_start: 0.8494 (mmtp) cc_final: 0.8260 (mttt) REVERT: Y 138 LYS cc_start: 0.7770 (mttt) cc_final: 0.7470 (mtpt) REVERT: Z 17 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7295 (pp) REVERT: Z 22 GLN cc_start: 0.8538 (pt0) cc_final: 0.7778 (pt0) REVERT: Z 68 LYS cc_start: 0.7826 (tttt) cc_final: 0.7553 (tttm) REVERT: a 50 PHE cc_start: 0.7474 (m-80) cc_final: 0.7225 (m-80) REVERT: a 64 ASN cc_start: 0.6448 (m-40) cc_final: 0.5892 (m110) REVERT: a 98 LYS cc_start: 0.7833 (tptt) cc_final: 0.7463 (tptp) REVERT: b 38 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7371 (mmtt) REVERT: b 66 LYS cc_start: 0.8034 (mttt) cc_final: 0.7772 (mttm) REVERT: b 85 ARG cc_start: 0.6961 (ttm170) cc_final: 0.6736 (ttm110) REVERT: c 34 ASP cc_start: 0.7373 (m-30) cc_final: 0.7003 (m-30) REVERT: c 45 THR cc_start: 0.8380 (m) cc_final: 0.8093 (t) REVERT: c 57 VAL cc_start: 0.4633 (m) cc_final: 0.4386 (p) REVERT: c 75 GLU cc_start: 0.3889 (tp30) cc_final: 0.3590 (tp30) REVERT: d 16 LYS cc_start: 0.7424 (tttt) cc_final: 0.7185 (ttpt) REVERT: d 38 THR cc_start: 0.6003 (t) cc_final: 0.5614 (p) REVERT: d 43 ILE cc_start: 0.8402 (mt) cc_final: 0.7966 (pt) REVERT: e 13 LYS cc_start: 0.8225 (mttm) cc_final: 0.7959 (mtpt) REVERT: f 125 LYS cc_start: 0.6528 (mttt) cc_final: 0.6106 (mmtt) REVERT: h 4 GLN cc_start: 0.3343 (tt0) cc_final: 0.3000 (tp40) REVERT: h 5 MET cc_start: 0.5603 (mmp) cc_final: 0.3994 (mmt) REVERT: h 26 GLN cc_start: 0.7472 (mm110) cc_final: 0.5981 (tp40) REVERT: h 36 ARG cc_start: 0.7393 (tpp80) cc_final: 0.7035 (tpt170) REVERT: h 45 LEU cc_start: 0.8529 (mt) cc_final: 0.8289 (mt) REVERT: h 57 ARG cc_start: 0.6113 (tpp80) cc_final: 0.5862 (mmt90) REVERT: h 100 ARG cc_start: 0.6929 (ttp-110) cc_final: 0.6619 (ttp80) REVERT: h 119 GLN cc_start: 0.6852 (mm110) cc_final: 0.6086 (mt0) REVERT: h 122 SER cc_start: 0.8153 (m) cc_final: 0.7915 (p) REVERT: h 155 ARG cc_start: 0.7420 (mmt-90) cc_final: 0.7010 (mmm160) REVERT: h 178 ASN cc_start: 0.6329 (OUTLIER) cc_final: 0.5831 (t0) REVERT: h 215 GLN cc_start: 0.5647 (mm-40) cc_final: 0.5398 (mm-40) REVERT: h 217 MET cc_start: 0.7366 (mtt) cc_final: 0.7141 (mtt) REVERT: h 231 ASP cc_start: 0.7669 (p0) cc_final: 0.7402 (t70) REVERT: h 247 TRP cc_start: 0.6597 (m-10) cc_final: 0.6308 (m-10) REVERT: h 259 TRP cc_start: 0.5164 (m-90) cc_final: 0.4886 (m100) REVERT: h 270 LEU cc_start: 0.6669 (mt) cc_final: 0.6267 (mt) REVERT: h 285 GLN cc_start: 0.7598 (pt0) cc_final: 0.6640 (mt0) REVERT: h 286 CYS cc_start: 0.7904 (t) cc_final: 0.7604 (t) REVERT: n 17 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7413 (mtt90) REVERT: n 20 MET cc_start: 0.6755 (mmt) cc_final: 0.6447 (tmm) outliers start: 91 outliers final: 21 residues processed: 1584 average time/residue: 0.8860 time to fit residues: 2239.2019 Evaluate side-chains 1075 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1041 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 137 SER Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 118 GLU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain T residue 142 ARG Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain V residue 36 CYS Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain a residue 111 ARG Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain h residue 178 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 2.9990 chunk 500 optimal weight: 10.0000 chunk 277 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 337 optimal weight: 3.9990 chunk 267 optimal weight: 20.0000 chunk 517 optimal weight: 0.0980 chunk 200 optimal weight: 7.9990 chunk 314 optimal weight: 0.7980 chunk 385 optimal weight: 1.9990 chunk 599 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 128 GLN C 53 GLN C 157 GLN C 177 GLN C 232 HIS D 115 GLN D 120 GLN E 145 GLN E 174 HIS F 67 GLN G 83 ASN G 118 ASN H 70 HIS I 73 GLN I 162 GLN J 7 ASN J 35 ASN J 138 ASN J 168 GLN L 61 GLN M 83 GLN M 112 HIS N 48 HIS O 36 GLN P 32 HIS Q 104 GLN R 48 GLN R 86 GLN S 83 ASN S 127 ASN T 11 HIS U 85 ASN V 47 ASN V 81 GLN W 82 ASN X 15 ASN X 16 ASN X 24 GLN X 64 ASN X 98 GLN X 113 HIS ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN Z 63 HIS Z 106 GLN c 26 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 GLN g 93 HIS h 14 HIS h 119 GLN h 178 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 84823 Z= 0.176 Angle : 0.632 9.853 123619 Z= 0.328 Chirality : 0.039 0.571 15363 Planarity : 0.004 0.039 8630 Dihedral : 24.190 179.980 35110 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 4.15 % Allowed : 12.64 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 4788 helix: -0.19 (0.12), residues: 1553 sheet: -1.91 (0.16), residues: 886 loop : -1.64 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP h 17 HIS 0.011 0.001 HIS H 70 PHE 0.033 0.002 PHE S 111 TYR 0.018 0.001 TYR h 246 ARG 0.008 0.001 ARG Z 61 *********************** 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 1288 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1114 time to evaluate : 4.293 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: B 44 ASP cc_start: 0.7120 (t70) cc_final: 0.6846 (t0) REVERT: B 52 LYS cc_start: 0.7800 (tttt) cc_final: 0.7545 (ttpt) REVERT: B 69 GLU cc_start: 0.7947 (tt0) cc_final: 0.7332 (tp30) REVERT: B 75 SER cc_start: 0.8907 (t) cc_final: 0.8634 (m) REVERT: B 80 ARG cc_start: 0.6478 (mtp-110) cc_final: 0.6270 (mtm110) REVERT: B 109 THR cc_start: 0.8511 (m) cc_final: 0.7844 (p) REVERT: B 112 ILE cc_start: 0.8231 (mt) cc_final: 0.7710 (tt) REVERT: B 136 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: B 144 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8467 (t) REVERT: B 176 TRP cc_start: 0.7851 (t60) cc_final: 0.7461 (t60) REVERT: B 181 GLU cc_start: 0.7527 (tp30) cc_final: 0.7206 (tp30) REVERT: B 192 GLU cc_start: 0.6331 (mm-30) cc_final: 0.5639 (mp0) REVERT: B 209 GLU cc_start: 0.4710 (mt-10) cc_final: 0.4230 (tp30) REVERT: C 83 LYS cc_start: 0.7266 (mtmt) cc_final: 0.6852 (mtmt) REVERT: C 95 ASN cc_start: 0.7612 (t0) cc_final: 0.7156 (t0) REVERT: C 118 GLN cc_start: 0.8514 (pt0) cc_final: 0.8161 (pt0) REVERT: C 122 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8119 (mt-10) REVERT: C 144 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7354 (tttm) REVERT: C 149 GLN cc_start: 0.8286 (tt0) cc_final: 0.8069 (tt0) REVERT: C 182 LYS cc_start: 0.7199 (tmtt) cc_final: 0.6826 (mtmt) REVERT: C 196 ASP cc_start: 0.7960 (t0) cc_final: 0.7733 (t0) REVERT: C 230 GLU cc_start: 0.7260 (tt0) cc_final: 0.6952 (tp30) REVERT: D 68 ARG cc_start: 0.7068 (tpt90) cc_final: 0.6285 (mmm160) REVERT: D 73 MET cc_start: 0.7306 (mpt) cc_final: 0.7050 (mmm) REVERT: D 79 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7826 (mm-30) REVERT: D 90 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7311 (mt-10) REVERT: D 144 SER cc_start: 0.8236 (t) cc_final: 0.7770 (m) REVERT: D 161 SER cc_start: 0.9003 (t) cc_final: 0.8740 (p) REVERT: E 14 ASP cc_start: 0.8053 (t0) cc_final: 0.7750 (t0) REVERT: E 31 GLU cc_start: 0.7228 (pm20) cc_final: 0.6711 (pm20) REVERT: E 65 ARG cc_start: 0.4825 (mtp85) cc_final: 0.4380 (ttp-170) REVERT: E 85 GLU cc_start: 0.6738 (pt0) cc_final: 0.6221 (tm-30) REVERT: E 87 TYR cc_start: 0.6359 (m-80) cc_final: 0.5603 (m-80) REVERT: E 89 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6241 (tt0) REVERT: E 117 ARG cc_start: 0.7229 (tpt-90) cc_final: 0.6397 (ttm110) REVERT: E 120 TYR cc_start: 0.7876 (m-80) cc_final: 0.6309 (t80) REVERT: E 146 ARG cc_start: 0.7329 (tpp80) cc_final: 0.5536 (ptm160) REVERT: F 7 LYS cc_start: 0.7988 (mttt) cc_final: 0.7648 (mtmt) REVERT: F 32 SER cc_start: 0.8720 (t) cc_final: 0.8481 (p) REVERT: F 39 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7565 (mtp-110) REVERT: F 47 PHE cc_start: 0.8432 (t80) cc_final: 0.8197 (t80) REVERT: F 79 ASP cc_start: 0.7306 (t0) cc_final: 0.6707 (t70) REVERT: F 97 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6482 (mm-30) REVERT: F 163 ASP cc_start: 0.7118 (t0) cc_final: 0.6837 (t0) REVERT: F 205 PHE cc_start: 0.7264 (m-80) cc_final: 0.6897 (m-10) REVERT: F 221 ARG cc_start: 0.7559 (ttm170) cc_final: 0.6964 (mtt180) REVERT: F 232 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7682 (t0) REVERT: F 255 ARG cc_start: 0.7156 (ttp80) cc_final: 0.6883 (ptm-80) REVERT: G 20 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6633 (t80) REVERT: G 37 ASP cc_start: 0.8280 (t70) cc_final: 0.7908 (m-30) REVERT: G 44 LYS cc_start: 0.7072 (tttt) cc_final: 0.6703 (mmtt) REVERT: G 59 LYS cc_start: 0.8277 (ttmt) cc_final: 0.8052 (mmtm) REVERT: G 65 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7870 (mm-40) REVERT: G 88 MET cc_start: 0.8562 (tmm) cc_final: 0.8305 (ttp) REVERT: G 94 LYS cc_start: 0.6849 (tttt) cc_final: 0.6539 (ttpp) REVERT: G 103 LEU cc_start: 0.8179 (tp) cc_final: 0.7973 (tp) REVERT: G 160 GLU cc_start: 0.7411 (tt0) cc_final: 0.7103 (tt0) REVERT: H 12 CYS cc_start: 0.5944 (t) cc_final: 0.5544 (m) REVERT: H 17 GLU cc_start: 0.7041 (pt0) cc_final: 0.6735 (tt0) REVERT: H 31 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5969 (ttm110) REVERT: H 44 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7199 (mt-10) REVERT: H 57 ASP cc_start: 0.6651 (t70) cc_final: 0.6148 (t0) REVERT: H 89 THR cc_start: 0.8725 (m) cc_final: 0.8453 (p) REVERT: H 114 VAL cc_start: 0.7724 (t) cc_final: 0.7436 (m) REVERT: H 121 ILE cc_start: 0.5209 (tp) cc_final: 0.4972 (mm) REVERT: H 131 ARG cc_start: 0.5253 (mpt90) cc_final: 0.4880 (mtm110) REVERT: H 154 ARG cc_start: 0.6423 (mpt-90) cc_final: 0.6159 (mpp80) REVERT: H 190 ARG cc_start: 0.6788 (tpt-90) cc_final: 0.6468 (tpt90) REVERT: H 200 LYS cc_start: 0.7098 (tttt) cc_final: 0.6607 (mptt) REVERT: H 203 LYS cc_start: 0.7566 (tttt) cc_final: 0.7000 (ptmt) REVERT: H 217 MET cc_start: 0.6565 (tpp) cc_final: 0.6066 (mmp) REVERT: I 15 LYS cc_start: 0.6531 (mttm) cc_final: 0.6240 (mptt) REVERT: I 57 ARG cc_start: 0.4527 (mmm-85) cc_final: 0.4138 (mmp80) REVERT: I 99 ARG cc_start: 0.6438 (ttt180) cc_final: 0.6151 (tpm170) REVERT: I 105 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.7240 (p) REVERT: I 107 LYS cc_start: 0.5639 (mttt) cc_final: 0.5335 (pttt) REVERT: I 155 LYS cc_start: 0.6338 (mttt) cc_final: 0.6102 (mtmt) REVERT: I 162 GLN cc_start: 0.6501 (mp10) cc_final: 0.6263 (mp10) REVERT: I 163 GLN cc_start: 0.6701 (tt0) cc_final: 0.6009 (tm-30) REVERT: J 46 VAL cc_start: 0.8297 (t) cc_final: 0.8070 (p) REVERT: J 64 ASN cc_start: 0.7251 (t0) cc_final: 0.6829 (t0) REVERT: J 77 ARG cc_start: 0.7093 (ttp-170) cc_final: 0.6594 (ttm170) REVERT: J 83 TYR cc_start: 0.7914 (t80) cc_final: 0.7058 (t80) REVERT: J 91 VAL cc_start: 0.7237 (t) cc_final: 0.6890 (t) REVERT: J 92 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.6968 (ttp80) REVERT: J 95 THR cc_start: 0.8515 (m) cc_final: 0.8194 (p) REVERT: J 144 LYS cc_start: 0.7121 (ptpt) cc_final: 0.6453 (mmtt) REVERT: J 157 LYS cc_start: 0.7115 (tttt) cc_final: 0.6591 (mmtm) REVERT: J 163 GLU cc_start: 0.7647 (tt0) cc_final: 0.7440 (tm-30) REVERT: J 167 GLN cc_start: 0.6735 (tt0) cc_final: 0.6485 (tp40) REVERT: J 200 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7816 (ttm-80) REVERT: K 17 ARG cc_start: 0.7755 (ttt90) cc_final: 0.6853 (ttm-80) REVERT: K 18 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7673 (mmt180) REVERT: K 34 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6201 (mp0) REVERT: K 92 MET cc_start: 0.7707 (ttt) cc_final: 0.7459 (ttm) REVERT: K 101 LYS cc_start: 0.7424 (ptmt) cc_final: 0.7182 (mmmt) REVERT: K 138 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6781 (mtt-85) REVERT: K 154 GLN cc_start: 0.7360 (tt0) cc_final: 0.7144 (tt0) REVERT: L 16 PHE cc_start: 0.7120 (t80) cc_final: 0.6821 (t80) REVERT: L 26 ASP cc_start: 0.8228 (t0) cc_final: 0.7555 (t0) REVERT: L 29 MET cc_start: 0.7061 (ttm) cc_final: 0.6729 (ttm) REVERT: L 89 ILE cc_start: 0.4778 (OUTLIER) cc_final: 0.4552 (tp) REVERT: M 45 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7693 (mtpt) REVERT: M 84 ARG cc_start: 0.7241 (mmt90) cc_final: 0.6915 (mtt90) REVERT: M 97 ARG cc_start: 0.7253 (ptt90) cc_final: 0.6662 (ttt90) REVERT: M 109 MET cc_start: 0.8293 (ptp) cc_final: 0.7798 (ptp) REVERT: N 102 LYS cc_start: 0.4291 (ttpt) cc_final: 0.3637 (tttp) REVERT: N 112 LYS cc_start: 0.6047 (tmtt) cc_final: 0.4703 (ptpt) REVERT: O 19 ARG cc_start: 0.7295 (ppt170) cc_final: 0.6965 (mtm180) REVERT: O 27 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.5833 (mmtp) REVERT: O 35 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6769 (tp30) REVERT: O 43 LYS cc_start: 0.6839 (ttpt) cc_final: 0.6623 (mtpp) REVERT: O 48 SER cc_start: 0.7633 (m) cc_final: 0.7427 (p) REVERT: O 75 LEU cc_start: 0.7102 (mp) cc_final: 0.6724 (mp) REVERT: O 106 ARG cc_start: 0.7705 (mmt90) cc_final: 0.7092 (ttp-110) REVERT: O 107 LYS cc_start: 0.6857 (tppp) cc_final: 0.6458 (mptt) REVERT: P 54 CYS cc_start: 0.7728 (t) cc_final: 0.7378 (p) REVERT: P 63 LYS cc_start: 0.8191 (mmtp) cc_final: 0.7780 (ptpp) REVERT: P 75 MET cc_start: 0.7162 (ttp) cc_final: 0.6687 (tmm) REVERT: P 80 ASP cc_start: 0.8110 (t0) cc_final: 0.7817 (t0) REVERT: P 107 THR cc_start: 0.7662 (m) cc_final: 0.7169 (t) REVERT: P 143 LYS cc_start: 0.8119 (tmmt) cc_final: 0.7510 (tppt) REVERT: Q 34 MET cc_start: 0.7836 (mtt) cc_final: 0.7537 (mtp) REVERT: Q 86 LEU cc_start: 0.7573 (mt) cc_final: 0.7319 (mp) REVERT: Q 101 THR cc_start: 0.7843 (m) cc_final: 0.7569 (p) REVERT: Q 108 LYS cc_start: 0.7424 (ptpt) cc_final: 0.6875 (mmtt) REVERT: Q 111 MET cc_start: 0.7451 (mmt) cc_final: 0.6797 (mmt) REVERT: Q 122 THR cc_start: 0.5972 (OUTLIER) cc_final: 0.5450 (m) REVERT: R 26 LYS cc_start: 0.5243 (ptmt) cc_final: 0.4899 (ptmt) REVERT: R 27 ARG cc_start: 0.5545 (ptp-110) cc_final: 0.5263 (ttp80) REVERT: R 43 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7158 (mm-30) REVERT: R 109 LYS cc_start: 0.7325 (ttmm) cc_final: 0.7050 (tttt) REVERT: R 114 GLN cc_start: 0.7460 (mt0) cc_final: 0.7253 (tm-30) REVERT: R 116 ASP cc_start: 0.6908 (t70) cc_final: 0.6668 (t70) REVERT: S 27 ASP cc_start: 0.8084 (t70) cc_final: 0.7634 (t0) REVERT: S 40 ILE cc_start: 0.7060 (mt) cc_final: 0.6766 (pt) REVERT: S 41 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6738 (mp) REVERT: S 62 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7357 (mt0) REVERT: S 81 ARG cc_start: 0.6870 (tmm-80) cc_final: 0.6444 (ttp-170) REVERT: S 97 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6815 (mm-30) REVERT: S 121 GLN cc_start: 0.5326 (pp30) cc_final: 0.5001 (mm-40) REVERT: S 126 MET cc_start: 0.5536 (ttp) cc_final: 0.5261 (ptm) REVERT: T 4 VAL cc_start: 0.6202 (m) cc_final: 0.5797 (t) REVERT: T 21 ASP cc_start: 0.8126 (t0) cc_final: 0.7770 (t0) REVERT: T 24 ARG cc_start: 0.6852 (mtp85) cc_final: 0.6545 (mtm-85) REVERT: T 46 ARG cc_start: 0.6920 (tpp-160) cc_final: 0.5874 (tpt90) REVERT: T 63 GLU cc_start: 0.6622 (tt0) cc_final: 0.6216 (tp30) REVERT: T 78 LYS cc_start: 0.7409 (ttmt) cc_final: 0.7088 (tptt) REVERT: T 112 GLU cc_start: 0.7422 (tt0) cc_final: 0.6599 (tm-30) REVERT: U 27 LYS cc_start: 0.7222 (ptpp) cc_final: 0.6896 (ptpt) REVERT: U 35 ASP cc_start: 0.7559 (m-30) cc_final: 0.7346 (m-30) REVERT: U 122 LYS cc_start: 0.7587 (ptmt) cc_final: 0.7024 (ptmt) REVERT: U 137 GLN cc_start: 0.7670 (mt0) cc_final: 0.7353 (mt0) REVERT: V 44 LYS cc_start: 0.6322 (mmtp) cc_final: 0.5837 (mmmt) REVERT: V 47 ASN cc_start: 0.7031 (t0) cc_final: 0.6499 (m-40) REVERT: V 56 MET cc_start: 0.8703 (tpp) cc_final: 0.8338 (tpp) REVERT: V 81 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: V 87 ARG cc_start: 0.6741 (mmt-90) cc_final: 0.6524 (mmt-90) REVERT: W 1 MET cc_start: 0.6631 (mpp) cc_final: 0.6147 (tpt) REVERT: W 11 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6850 (pp) REVERT: W 15 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7925 (mtp180) REVERT: W 21 ASN cc_start: 0.7995 (t0) cc_final: 0.6995 (t0) REVERT: W 34 MET cc_start: 0.7366 (ttp) cc_final: 0.6963 (ttm) REVERT: W 40 ASP cc_start: 0.6013 (m-30) cc_final: 0.5742 (m-30) REVERT: W 45 ARG cc_start: 0.7009 (mtt180) cc_final: 0.6470 (mtp180) REVERT: X 14 ILE cc_start: 0.8208 (pt) cc_final: 0.7920 (mt) REVERT: X 117 ARG cc_start: 0.6705 (tpp80) cc_final: 0.6285 (mtt-85) REVERT: Y 37 LYS cc_start: 0.6424 (tptt) cc_final: 0.6186 (mmmt) REVERT: Y 97 ASN cc_start: 0.7593 (m-40) cc_final: 0.7298 (m-40) REVERT: Y 135 LYS cc_start: 0.8476 (mmtp) cc_final: 0.8262 (mtpt) REVERT: Y 138 LYS cc_start: 0.8162 (mttt) cc_final: 0.7863 (mtpt) REVERT: Z 17 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7715 (pp) REVERT: Z 22 GLN cc_start: 0.8530 (pt0) cc_final: 0.7890 (pt0) REVERT: Z 68 LYS cc_start: 0.7929 (tttt) cc_final: 0.7659 (tttm) REVERT: Z 74 MET cc_start: 0.7896 (mtm) cc_final: 0.7631 (mtm) REVERT: Z 96 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7109 (pp) REVERT: a 50 PHE cc_start: 0.7231 (m-80) cc_final: 0.7007 (m-80) REVERT: a 111 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5479 (ptt180) REVERT: b 25 ASN cc_start: 0.8265 (t0) cc_final: 0.8061 (t0) REVERT: b 38 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7371 (mmtt) REVERT: b 59 PHE cc_start: 0.7252 (m-80) cc_final: 0.7022 (m-80) REVERT: b 86 ASN cc_start: 0.8615 (p0) cc_final: 0.8409 (p0) REVERT: c 34 ASP cc_start: 0.7388 (m-30) cc_final: 0.6917 (m-30) REVERT: c 45 THR cc_start: 0.8398 (m) cc_final: 0.8142 (t) REVERT: c 75 GLU cc_start: 0.4498 (tp30) cc_final: 0.4168 (tp30) REVERT: e 13 LYS cc_start: 0.8336 (mttm) cc_final: 0.8107 (mtpt) REVERT: e 38 MET cc_start: 0.8258 (ttt) cc_final: 0.7841 (ttm) REVERT: f 125 LYS cc_start: 0.6549 (mttt) cc_final: 0.6128 (mmtt) REVERT: h 4 GLN cc_start: 0.3390 (tt0) cc_final: 0.2862 (tp40) REVERT: h 5 MET cc_start: 0.5243 (mmp) cc_final: 0.4402 (mmt) REVERT: h 26 GLN cc_start: 0.7445 (mm110) cc_final: 0.6033 (tp40) REVERT: h 100 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6778 (ttp80) REVERT: h 122 SER cc_start: 0.7544 (m) cc_final: 0.7300 (p) REVERT: h 231 ASP cc_start: 0.7499 (p0) cc_final: 0.6984 (t0) REVERT: h 259 TRP cc_start: 0.5115 (m-90) cc_final: 0.4882 (m-90) REVERT: h 285 GLN cc_start: 0.7276 (pt0) cc_final: 0.6392 (mt0) REVERT: h 286 CYS cc_start: 0.7656 (t) cc_final: 0.7291 (t) REVERT: n 17 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7278 (mtt90) outliers start: 174 outliers final: 94 residues processed: 1208 average time/residue: 0.8889 time to fit residues: 1750.3368 Evaluate side-chains 1057 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 947 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 36 SER 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 Q residue 15 PHE Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 118 GLU Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 81 GLN Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 111 ARG Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 100 LYS Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 167 SER Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 203 ASP Chi-restraints excluded: chain h residue 257 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 498 optimal weight: 0.7980 chunk 408 optimal weight: 0.6980 chunk 165 optimal weight: 8.9990 chunk 600 optimal weight: 7.9990 chunk 648 optimal weight: 7.9990 chunk 534 optimal weight: 0.1980 chunk 595 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 481 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 128 GLN B 180 GLN C 53 GLN C 177 GLN F 179 ASN G 83 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 7 ASN K 124 HIS L 61 GLN M 19 ASN M 100 ASN N 19 GLN P 32 HIS ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 ASN Y 73 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN c 49 HIS c 51 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 ASN f 110 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 84823 Z= 0.193 Angle : 0.595 10.717 123619 Z= 0.305 Chirality : 0.038 0.518 15363 Planarity : 0.004 0.047 8630 Dihedral : 24.010 179.807 35092 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 4.77 % Allowed : 13.69 % Favored : 81.54 % 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: -1.17 (0.12), residues: 4788 helix: 0.58 (0.13), residues: 1554 sheet: -1.50 (0.16), residues: 879 loop : -1.39 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP h 17 HIS 0.033 0.001 HIS T 11 PHE 0.019 0.002 PHE Q 119 TYR 0.017 0.002 TYR h 246 ARG 0.008 0.001 ARG Z 61 *********************** 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 1166 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 966 time to evaluate : 5.816 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 52 LYS cc_start: 0.7781 (tttt) cc_final: 0.7531 (ttpt) REVERT: B 69 GLU cc_start: 0.7977 (tt0) cc_final: 0.7470 (tp30) REVERT: B 75 SER cc_start: 0.8929 (t) cc_final: 0.8610 (m) REVERT: B 78 SER cc_start: 0.8959 (t) cc_final: 0.8569 (t) REVERT: B 80 ARG cc_start: 0.6551 (mtp-110) cc_final: 0.6294 (mtm180) REVERT: B 109 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8020 (p) REVERT: B 144 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8384 (t) REVERT: B 192 GLU cc_start: 0.6298 (mm-30) cc_final: 0.5552 (mp0) REVERT: C 83 LYS cc_start: 0.7339 (mtmt) cc_final: 0.7053 (mttt) REVERT: C 89 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7234 (mm-30) REVERT: C 95 ASN cc_start: 0.7663 (t0) cc_final: 0.7273 (t0) REVERT: C 122 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8192 (mt-10) REVERT: C 144 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7329 (tttm) REVERT: C 177 GLN cc_start: 0.7358 (mt0) cc_final: 0.7119 (mt0) REVERT: C 182 LYS cc_start: 0.7186 (tmtt) cc_final: 0.6782 (mtmt) REVERT: C 230 GLU cc_start: 0.7297 (tt0) cc_final: 0.6969 (tp30) REVERT: D 92 GLU cc_start: 0.7581 (mp0) cc_final: 0.7171 (mp0) REVERT: D 144 SER cc_start: 0.8202 (t) cc_final: 0.7733 (m) REVERT: D 161 SER cc_start: 0.8966 (t) cc_final: 0.8659 (p) REVERT: D 215 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6856 (mp) REVERT: E 1 MET cc_start: 0.5290 (ttt) cc_final: 0.4563 (pmm) REVERT: E 14 ASP cc_start: 0.8061 (t0) cc_final: 0.7806 (t0) REVERT: E 31 GLU cc_start: 0.7097 (pm20) cc_final: 0.6619 (pm20) REVERT: E 85 GLU cc_start: 0.6737 (pt0) cc_final: 0.6456 (pt0) REVERT: E 87 TYR cc_start: 0.6176 (m-80) cc_final: 0.5393 (m-80) REVERT: E 89 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6008 (tt0) REVERT: E 113 LEU cc_start: 0.6448 (tp) cc_final: 0.6242 (tp) REVERT: E 117 ARG cc_start: 0.7292 (tpt-90) cc_final: 0.6472 (ttm110) REVERT: E 120 TYR cc_start: 0.7950 (m-80) cc_final: 0.6273 (t80) REVERT: E 125 PHE cc_start: 0.7190 (t80) cc_final: 0.6669 (t80) REVERT: E 146 ARG cc_start: 0.7237 (tpp80) cc_final: 0.5437 (ptm160) REVERT: F 7 LYS cc_start: 0.8035 (mttt) cc_final: 0.7762 (mtmt) REVERT: F 32 SER cc_start: 0.8597 (t) cc_final: 0.8337 (p) REVERT: F 39 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7502 (mtp-110) REVERT: F 47 PHE cc_start: 0.8492 (t80) cc_final: 0.8284 (t80) REVERT: F 79 ASP cc_start: 0.7309 (t0) cc_final: 0.6617 (t70) REVERT: F 97 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6452 (mm-30) REVERT: F 163 ASP cc_start: 0.7081 (t0) cc_final: 0.6720 (t0) REVERT: F 205 PHE cc_start: 0.7432 (m-80) cc_final: 0.7140 (m-10) REVERT: F 221 ARG cc_start: 0.7570 (ttm170) cc_final: 0.7006 (mtt180) REVERT: F 232 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8026 (m110) REVERT: F 255 ARG cc_start: 0.7185 (ttp80) cc_final: 0.6879 (ptm-80) REVERT: G 20 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6457 (t80) REVERT: G 37 ASP cc_start: 0.8281 (t70) cc_final: 0.7909 (m-30) REVERT: G 56 TYR cc_start: 0.8396 (m-80) cc_final: 0.8027 (m-80) REVERT: G 59 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8119 (mmtm) REVERT: G 88 MET cc_start: 0.8655 (tmm) cc_final: 0.8452 (ttp) REVERT: G 94 LYS cc_start: 0.6869 (tttt) cc_final: 0.6574 (ttpp) REVERT: G 160 GLU cc_start: 0.7382 (tt0) cc_final: 0.7067 (tt0) REVERT: G 171 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7115 (mt-10) REVERT: H 12 CYS cc_start: 0.5874 (t) cc_final: 0.5468 (m) REVERT: H 17 GLU cc_start: 0.7022 (pt0) cc_final: 0.6718 (tt0) REVERT: H 24 LEU cc_start: 0.5708 (mt) cc_final: 0.5462 (mt) REVERT: H 31 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.6055 (ttm110) REVERT: H 44 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6953 (tt0) REVERT: H 57 ASP cc_start: 0.6864 (t70) cc_final: 0.6323 (t0) REVERT: H 89 THR cc_start: 0.8724 (m) cc_final: 0.8426 (p) REVERT: H 114 VAL cc_start: 0.7733 (t) cc_final: 0.7510 (m) REVERT: H 131 ARG cc_start: 0.5298 (mpt90) cc_final: 0.4765 (mtm110) REVERT: H 154 ARG cc_start: 0.6411 (mpt-90) cc_final: 0.6049 (mpp80) REVERT: H 200 LYS cc_start: 0.7109 (tttt) cc_final: 0.6560 (mptt) REVERT: H 203 LYS cc_start: 0.7566 (tttt) cc_final: 0.7002 (ptmt) REVERT: H 217 MET cc_start: 0.6572 (tpp) cc_final: 0.6045 (mmp) REVERT: I 15 LYS cc_start: 0.6584 (mttm) cc_final: 0.6334 (mptt) REVERT: I 57 ARG cc_start: 0.4559 (mmm-85) cc_final: 0.4150 (mmp80) REVERT: I 99 ARG cc_start: 0.6434 (ttt180) cc_final: 0.6125 (tpt170) REVERT: I 107 LYS cc_start: 0.5634 (mttt) cc_final: 0.5332 (pttt) REVERT: I 163 GLN cc_start: 0.6784 (tt0) cc_final: 0.6110 (tm-30) REVERT: J 38 ILE cc_start: 0.7199 (mt) cc_final: 0.6950 (mt) REVERT: J 46 VAL cc_start: 0.8293 (t) cc_final: 0.8042 (p) REVERT: J 77 ARG cc_start: 0.7170 (ttp-170) cc_final: 0.6529 (ttm170) REVERT: J 83 TYR cc_start: 0.7937 (t80) cc_final: 0.7119 (t80) REVERT: J 92 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.6847 (ttp80) REVERT: J 95 THR cc_start: 0.8416 (m) cc_final: 0.8084 (p) REVERT: J 141 ARG cc_start: 0.5188 (mmt-90) cc_final: 0.4821 (tpp-160) REVERT: J 144 LYS cc_start: 0.6984 (ptpt) cc_final: 0.6365 (mmtt) REVERT: J 157 LYS cc_start: 0.6944 (tttt) cc_final: 0.6475 (mmtm) REVERT: J 167 GLN cc_start: 0.6657 (tt0) cc_final: 0.6397 (tp40) REVERT: J 170 LYS cc_start: 0.6325 (mttt) cc_final: 0.5896 (mmtm) REVERT: J 200 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7817 (ttm-80) REVERT: K 17 ARG cc_start: 0.7746 (ttt90) cc_final: 0.6804 (ttm-80) REVERT: K 18 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7659 (mmt180) REVERT: K 34 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6234 (mp0) REVERT: K 101 LYS cc_start: 0.7453 (ptmt) cc_final: 0.7161 (mmmt) REVERT: K 138 ARG cc_start: 0.7303 (mtt180) cc_final: 0.6858 (mtt-85) REVERT: L 16 PHE cc_start: 0.7112 (t80) cc_final: 0.6865 (t80) REVERT: L 26 ASP cc_start: 0.8175 (t0) cc_final: 0.7481 (t0) REVERT: L 29 MET cc_start: 0.6984 (ttm) cc_final: 0.6656 (ttm) REVERT: L 89 ILE cc_start: 0.4762 (OUTLIER) cc_final: 0.4457 (tp) REVERT: M 45 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7714 (mtpt) REVERT: M 84 ARG cc_start: 0.7296 (mmt90) cc_final: 0.6820 (mtt90) REVERT: M 97 ARG cc_start: 0.7129 (ptt90) cc_final: 0.6429 (ttt90) REVERT: M 108 ASN cc_start: 0.7096 (p0) cc_final: 0.6746 (p0) REVERT: M 109 MET cc_start: 0.8335 (ptp) cc_final: 0.7811 (ptp) REVERT: N 102 LYS cc_start: 0.4581 (ttpt) cc_final: 0.4131 (mmmt) REVERT: N 112 LYS cc_start: 0.6147 (tmtt) cc_final: 0.4695 (ptpt) REVERT: O 19 ARG cc_start: 0.7306 (ppt170) cc_final: 0.6942 (mtm180) REVERT: O 27 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.5869 (mmtp) REVERT: O 35 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6768 (tp30) REVERT: O 48 SER cc_start: 0.7673 (m) cc_final: 0.7420 (p) REVERT: O 106 ARG cc_start: 0.7769 (mmt90) cc_final: 0.7144 (ttp-110) REVERT: O 107 LYS cc_start: 0.6774 (tppp) cc_final: 0.6562 (mptt) REVERT: P 54 CYS cc_start: 0.7564 (t) cc_final: 0.7282 (p) REVERT: P 63 LYS cc_start: 0.8136 (mmtp) cc_final: 0.7763 (ptpp) REVERT: P 75 MET cc_start: 0.7296 (ttp) cc_final: 0.6844 (tmm) REVERT: P 80 ASP cc_start: 0.8080 (t0) cc_final: 0.7847 (t0) REVERT: P 107 THR cc_start: 0.7758 (m) cc_final: 0.7499 (t) REVERT: P 138 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6830 (m-30) REVERT: P 143 LYS cc_start: 0.8048 (tmmt) cc_final: 0.7493 (tppt) REVERT: Q 34 MET cc_start: 0.7881 (mtt) cc_final: 0.7673 (mtp) REVERT: Q 101 THR cc_start: 0.7946 (m) cc_final: 0.7688 (p) REVERT: Q 108 LYS cc_start: 0.7305 (ptpt) cc_final: 0.6841 (mmtp) REVERT: Q 111 MET cc_start: 0.7575 (mmt) cc_final: 0.6793 (mmt) REVERT: R 43 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7153 (mm-30) REVERT: R 116 ASP cc_start: 0.6894 (t70) cc_final: 0.6644 (t70) REVERT: S 62 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7382 (mt0) REVERT: S 67 ARG cc_start: 0.6054 (mtp85) cc_final: 0.5807 (ttp80) REVERT: S 80 ARG cc_start: 0.6443 (tmm-80) cc_final: 0.6097 (tmm-80) REVERT: S 81 ARG cc_start: 0.6999 (tmm-80) cc_final: 0.6680 (ttm170) REVERT: S 97 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6713 (mm-30) REVERT: S 118 GLN cc_start: 0.5839 (tp-100) cc_final: 0.5266 (tp-100) REVERT: T 21 ASP cc_start: 0.8143 (t0) cc_final: 0.7701 (t0) REVERT: T 24 ARG cc_start: 0.6819 (mtp85) cc_final: 0.6419 (mtm-85) REVERT: T 63 GLU cc_start: 0.7087 (tt0) cc_final: 0.6543 (tp30) REVERT: T 78 LYS cc_start: 0.7602 (ttmt) cc_final: 0.7217 (tptt) REVERT: T 112 GLU cc_start: 0.7513 (tt0) cc_final: 0.6583 (tm-30) REVERT: T 127 TRP cc_start: 0.7843 (m-10) cc_final: 0.7567 (m-10) REVERT: U 27 LYS cc_start: 0.7258 (ptpp) cc_final: 0.6925 (ptpt) REVERT: U 137 GLN cc_start: 0.7604 (mt0) cc_final: 0.7258 (mt0) REVERT: V 44 LYS cc_start: 0.6401 (mmtp) cc_final: 0.5949 (mmmt) REVERT: V 48 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6165 (pp) REVERT: W 1 MET cc_start: 0.6637 (mpp) cc_final: 0.6117 (tpt) REVERT: W 11 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6390 (pp) REVERT: W 21 ASN cc_start: 0.8218 (t0) cc_final: 0.7023 (t0) REVERT: W 34 MET cc_start: 0.7266 (ttp) cc_final: 0.7009 (ttm) REVERT: W 45 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6430 (mtp180) REVERT: X 14 ILE cc_start: 0.8117 (pt) cc_final: 0.7909 (mt) REVERT: X 117 ARG cc_start: 0.6789 (tpp80) cc_final: 0.6167 (mtt-85) REVERT: Y 37 LYS cc_start: 0.6461 (tptt) cc_final: 0.6179 (mmmt) REVERT: Y 97 ASN cc_start: 0.7654 (m-40) cc_final: 0.7363 (m-40) REVERT: Y 135 LYS cc_start: 0.8516 (mmtp) cc_final: 0.8293 (mttt) REVERT: Y 138 LYS cc_start: 0.8126 (mttt) cc_final: 0.7778 (mtpt) REVERT: Z 17 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7831 (pp) REVERT: Z 22 GLN cc_start: 0.8399 (pt0) cc_final: 0.8056 (pt0) REVERT: Z 68 LYS cc_start: 0.7805 (tttt) cc_final: 0.7553 (tttm) REVERT: Z 96 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7142 (pp) REVERT: a 64 ASN cc_start: 0.6316 (m-40) cc_final: 0.6028 (m-40) REVERT: a 88 LEU cc_start: 0.7644 (mt) cc_final: 0.7400 (mp) REVERT: b 38 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7381 (mmtt) REVERT: b 86 ASN cc_start: 0.8610 (p0) cc_final: 0.8376 (p0) REVERT: c 34 ASP cc_start: 0.7370 (m-30) cc_final: 0.7028 (m-30) REVERT: c 45 THR cc_start: 0.8342 (m) cc_final: 0.8020 (t) REVERT: c 75 GLU cc_start: 0.4487 (tp30) cc_final: 0.4177 (tp30) REVERT: e 13 LYS cc_start: 0.8478 (mttm) cc_final: 0.8062 (mtpt) REVERT: e 38 MET cc_start: 0.8320 (ttt) cc_final: 0.7866 (ttm) REVERT: f 125 LYS cc_start: 0.6477 (mttt) cc_final: 0.6114 (mmtt) REVERT: h 4 GLN cc_start: 0.3359 (tt0) cc_final: 0.2731 (tp40) REVERT: h 5 MET cc_start: 0.5214 (mmp) cc_final: 0.4594 (mmm) REVERT: h 26 GLN cc_start: 0.7447 (mm110) cc_final: 0.5794 (tp40) REVERT: h 100 ARG cc_start: 0.7104 (ttp-110) cc_final: 0.6789 (ttp80) REVERT: h 119 GLN cc_start: 0.6764 (mm-40) cc_final: 0.6329 (mm110) REVERT: h 231 ASP cc_start: 0.7266 (p0) cc_final: 0.7010 (t0) REVERT: h 272 GLN cc_start: 0.4558 (pm20) cc_final: 0.3289 (tp-100) REVERT: h 285 GLN cc_start: 0.7298 (pt0) cc_final: 0.6440 (mt0) REVERT: h 286 CYS cc_start: 0.7665 (t) cc_final: 0.7383 (t) outliers start: 200 outliers final: 122 residues processed: 1086 average time/residue: 0.8301 time to fit residues: 1484.9346 Evaluate side-chains 1030 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 895 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 81 ARG Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 89 ILE Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 36 SER Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 CYS Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 83 ASN Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 68 ILE Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 72 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 53 ILE Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 81 SER Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain d residue 57 THR Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 203 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 1.9990 chunk 451 optimal weight: 0.6980 chunk 311 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 286 optimal weight: 0.0470 chunk 403 optimal weight: 0.4980 chunk 602 optimal weight: 0.0870 chunk 637 optimal weight: 4.9990 chunk 314 optimal weight: 1.9990 chunk 571 optimal weight: 0.5980 chunk 171 optimal weight: 10.0000 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 HIS F 179 ASN H 59 GLN J 7 ASN M 100 ASN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS V 47 ASN Y 61 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN g 139 HIS h 226 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 84823 Z= 0.124 Angle : 0.542 9.676 123619 Z= 0.276 Chirality : 0.035 0.515 15363 Planarity : 0.004 0.044 8630 Dihedral : 23.859 179.722 35082 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 3.75 % Allowed : 15.77 % Favored : 80.49 % 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: -0.66 (0.12), residues: 4788 helix: 1.15 (0.13), residues: 1537 sheet: -1.18 (0.16), residues: 878 loop : -1.20 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP h 17 HIS 0.007 0.001 HIS T 11 PHE 0.022 0.001 PHE S 111 TYR 0.017 0.001 TYR O 38 ARG 0.008 0.000 ARG E 65 *********************** 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 1156 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 999 time to evaluate : 4.434 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: 0.7595 (tttt) cc_final: 0.7351 (ttpt) REVERT: B 69 GLU cc_start: 0.7756 (tt0) cc_final: 0.7195 (tp30) REVERT: B 75 SER cc_start: 0.8572 (t) cc_final: 0.8370 (m) REVERT: B 109 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8116 (p) REVERT: B 176 TRP cc_start: 0.7650 (t60) cc_final: 0.7273 (t60) REVERT: B 192 GLU cc_start: 0.6317 (mm-30) cc_final: 0.5615 (mp0) REVERT: C 83 LYS cc_start: 0.7433 (mtmt) cc_final: 0.7162 (mtmt) REVERT: C 89 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7193 (mm-30) REVERT: C 95 ASN cc_start: 0.7720 (t0) cc_final: 0.7428 (t0) REVERT: C 103 MET cc_start: 0.8534 (tmm) cc_final: 0.8224 (tmm) REVERT: C 144 LYS cc_start: 0.7985 (ttpt) cc_final: 0.7264 (tttm) REVERT: C 168 MET cc_start: 0.7902 (mtt) cc_final: 0.7695 (mtt) REVERT: C 177 GLN cc_start: 0.7347 (mt0) cc_final: 0.7110 (mt0) REVERT: C 182 LYS cc_start: 0.7104 (tmtt) cc_final: 0.6678 (mtmt) REVERT: C 230 GLU cc_start: 0.7336 (tt0) cc_final: 0.6970 (tp30) REVERT: D 61 LEU cc_start: 0.7432 (tp) cc_final: 0.6633 (mm) REVERT: D 79 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7685 (mm-30) REVERT: D 144 SER cc_start: 0.8213 (t) cc_final: 0.7707 (m) REVERT: D 161 SER cc_start: 0.8977 (t) cc_final: 0.8618 (p) REVERT: D 213 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7556 (mt) REVERT: D 215 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6872 (mp) REVERT: D 269 PHE cc_start: 0.8064 (m-80) cc_final: 0.7823 (m-80) REVERT: E 31 GLU cc_start: 0.7006 (pm20) cc_final: 0.6583 (pm20) REVERT: E 65 ARG cc_start: 0.5103 (mtp85) cc_final: 0.4879 (ttp-170) REVERT: E 83 SER cc_start: 0.6869 (t) cc_final: 0.6416 (m) REVERT: E 84 VAL cc_start: 0.7080 (OUTLIER) cc_final: 0.6812 (p) REVERT: E 85 GLU cc_start: 0.6459 (pt0) cc_final: 0.6072 (pt0) REVERT: E 87 TYR cc_start: 0.6087 (m-80) cc_final: 0.5305 (m-80) REVERT: E 89 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6295 (tt0) REVERT: E 117 ARG cc_start: 0.7147 (tpt-90) cc_final: 0.6346 (ttm110) REVERT: E 120 TYR cc_start: 0.7988 (m-80) cc_final: 0.6105 (t80) REVERT: E 125 PHE cc_start: 0.7182 (t80) cc_final: 0.6975 (t80) REVERT: E 146 ARG cc_start: 0.7311 (tpp80) cc_final: 0.5422 (ptm160) REVERT: F 7 LYS cc_start: 0.7967 (mttt) cc_final: 0.7680 (mtmt) REVERT: F 32 SER cc_start: 0.8462 (t) cc_final: 0.8209 (p) REVERT: F 39 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7345 (mtp-110) REVERT: F 49 ARG cc_start: 0.7480 (ptt90) cc_final: 0.7206 (ttp-170) REVERT: F 79 ASP cc_start: 0.7294 (t0) cc_final: 0.6971 (t0) REVERT: F 87 MET cc_start: 0.7804 (mmt) cc_final: 0.7498 (mmt) REVERT: F 97 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6372 (mm-30) REVERT: F 163 ASP cc_start: 0.7089 (t0) cc_final: 0.6757 (t0) REVERT: F 205 PHE cc_start: 0.7346 (m-80) cc_final: 0.7089 (m-10) REVERT: F 221 ARG cc_start: 0.7553 (ttm170) cc_final: 0.7249 (mmt90) REVERT: F 240 ARG cc_start: 0.6579 (ttp-110) cc_final: 0.4960 (tmm160) REVERT: F 255 ARG cc_start: 0.7128 (ttp80) cc_final: 0.6822 (ptm-80) REVERT: G 37 ASP cc_start: 0.8268 (t70) cc_final: 0.7888 (m-30) REVERT: G 56 TYR cc_start: 0.8390 (m-80) cc_final: 0.7997 (m-80) REVERT: G 160 GLU cc_start: 0.7267 (tt0) cc_final: 0.6908 (tt0) REVERT: G 166 ILE cc_start: 0.8360 (mt) cc_final: 0.8133 (tt) REVERT: H 12 CYS cc_start: 0.5818 (t) cc_final: 0.5351 (m) REVERT: H 44 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7040 (tt0) REVERT: H 46 LYS cc_start: 0.5992 (ptmt) cc_final: 0.5622 (ttpt) REVERT: H 57 ASP cc_start: 0.6651 (t70) cc_final: 0.6428 (t0) REVERT: H 89 THR cc_start: 0.8698 (m) cc_final: 0.8290 (p) REVERT: H 131 ARG cc_start: 0.5187 (mpt90) cc_final: 0.4647 (mtm110) REVERT: H 154 ARG cc_start: 0.6477 (mpt-90) cc_final: 0.6164 (mpp80) REVERT: H 190 ARG cc_start: 0.6841 (tpt-90) cc_final: 0.6507 (tpt90) REVERT: H 200 LYS cc_start: 0.7119 (tttt) cc_final: 0.6566 (mptt) REVERT: H 203 LYS cc_start: 0.7498 (tttt) cc_final: 0.6898 (ptmt) REVERT: H 217 MET cc_start: 0.6538 (tpp) cc_final: 0.5968 (mmp) REVERT: I 57 ARG cc_start: 0.4498 (mmm-85) cc_final: 0.4079 (mmp80) REVERT: I 61 ILE cc_start: 0.5157 (pt) cc_final: 0.4855 (mp) REVERT: I 99 ARG cc_start: 0.6276 (ttt180) cc_final: 0.5930 (tpm170) REVERT: I 107 LYS cc_start: 0.5591 (mttt) cc_final: 0.5316 (pttt) REVERT: I 163 GLN cc_start: 0.6767 (tt0) cc_final: 0.6047 (tm-30) REVERT: J 3 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6874 (tp) REVERT: J 37 LYS cc_start: 0.7490 (mmmm) cc_final: 0.6922 (mptt) REVERT: J 77 ARG cc_start: 0.6735 (ttp-170) cc_final: 0.6248 (ttm170) REVERT: J 83 TYR cc_start: 0.7838 (t80) cc_final: 0.7018 (t80) REVERT: J 92 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.6872 (ptm-80) REVERT: J 95 THR cc_start: 0.8367 (m) cc_final: 0.8031 (p) REVERT: J 144 LYS cc_start: 0.6948 (ptpt) cc_final: 0.6357 (mmtt) REVERT: J 157 LYS cc_start: 0.6914 (tttt) cc_final: 0.6413 (mmtm) REVERT: J 167 GLN cc_start: 0.6637 (tt0) cc_final: 0.6339 (tp40) REVERT: J 200 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.7978 (ttp-110) REVERT: K 17 ARG cc_start: 0.7729 (ttt90) cc_final: 0.6832 (ttm-80) REVERT: K 18 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7568 (mmt180) REVERT: K 34 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6376 (mp0) REVERT: K 101 LYS cc_start: 0.7367 (ptmt) cc_final: 0.7129 (mmmt) REVERT: K 138 ARG cc_start: 0.7180 (mtt180) cc_final: 0.6778 (mtt-85) REVERT: L 26 ASP cc_start: 0.8133 (t0) cc_final: 0.7461 (t0) REVERT: M 45 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7744 (mtpt) REVERT: M 84 ARG cc_start: 0.7162 (mmt90) cc_final: 0.6893 (mtt90) REVERT: M 97 ARG cc_start: 0.6835 (ptt90) cc_final: 0.6086 (ttt90) REVERT: M 109 MET cc_start: 0.8214 (ptp) cc_final: 0.7789 (ptp) REVERT: N 102 LYS cc_start: 0.4733 (ttpt) cc_final: 0.4160 (mmmt) REVERT: N 112 LYS cc_start: 0.6115 (tmtt) cc_final: 0.5808 (tptp) REVERT: O 19 ARG cc_start: 0.7301 (ppt170) cc_final: 0.6911 (mtm180) REVERT: O 27 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.5911 (mmtp) REVERT: O 35 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6752 (tp30) REVERT: O 106 ARG cc_start: 0.7845 (mmt90) cc_final: 0.7198 (ttp-110) REVERT: P 60 MET cc_start: 0.7515 (mtm) cc_final: 0.7231 (mtm) REVERT: P 75 MET cc_start: 0.7193 (ttp) cc_final: 0.6807 (tmm) REVERT: P 80 ASP cc_start: 0.8019 (t0) cc_final: 0.7799 (t0) REVERT: P 107 THR cc_start: 0.7595 (m) cc_final: 0.7246 (t) REVERT: P 130 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7386 (tm-30) REVERT: P 143 LYS cc_start: 0.8014 (tmmt) cc_final: 0.7574 (tppt) REVERT: Q 34 MET cc_start: 0.7802 (mtt) cc_final: 0.7293 (mtt) REVERT: Q 35 GLN cc_start: 0.7973 (mt0) cc_final: 0.7207 (mp10) REVERT: Q 88 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: Q 108 LYS cc_start: 0.7302 (ptpt) cc_final: 0.6875 (mmtp) REVERT: Q 111 MET cc_start: 0.7194 (mmt) cc_final: 0.6105 (mmt) REVERT: R 43 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7098 (mm-30) REVERT: R 68 ILE cc_start: 0.8494 (mt) cc_final: 0.8071 (mm) REVERT: R 102 GLU cc_start: 0.7655 (tt0) cc_final: 0.7236 (tp30) REVERT: R 129 SER cc_start: 0.8420 (p) cc_final: 0.8072 (m) REVERT: S 62 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7337 (mt0) REVERT: S 67 ARG cc_start: 0.5989 (mtp85) cc_final: 0.5754 (ttp80) REVERT: S 80 ARG cc_start: 0.6495 (tmm-80) cc_final: 0.6108 (tmm-80) REVERT: S 81 ARG cc_start: 0.7039 (tmm-80) cc_final: 0.6798 (ttm170) REVERT: S 97 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6518 (mm-30) REVERT: S 118 GLN cc_start: 0.5642 (tp-100) cc_final: 0.5273 (tp40) REVERT: T 21 ASP cc_start: 0.8181 (t0) cc_final: 0.7792 (t0) REVERT: T 24 ARG cc_start: 0.6956 (mtp85) cc_final: 0.6621 (mtm-85) REVERT: T 63 GLU cc_start: 0.6983 (tt0) cc_final: 0.6453 (tp30) REVERT: T 78 LYS cc_start: 0.7553 (ttmt) cc_final: 0.7193 (tptt) REVERT: T 91 LYS cc_start: 0.7592 (mttm) cc_final: 0.7026 (mmmt) REVERT: T 112 GLU cc_start: 0.7542 (tt0) cc_final: 0.6543 (tm-30) REVERT: T 127 TRP cc_start: 0.7843 (m-10) cc_final: 0.7600 (m-10) REVERT: U 27 LYS cc_start: 0.7239 (ptpp) cc_final: 0.6954 (ptpt) REVERT: U 98 SER cc_start: 0.8772 (t) cc_final: 0.7971 (p) REVERT: U 116 ASP cc_start: 0.7086 (t0) cc_final: 0.6844 (t0) REVERT: U 137 GLN cc_start: 0.7534 (mt0) cc_final: 0.7241 (mt0) REVERT: V 19 ARG cc_start: 0.4264 (mpt180) cc_final: 0.3310 (ttm170) REVERT: V 47 ASN cc_start: 0.6905 (OUTLIER) cc_final: 0.6331 (m-40) REVERT: W 11 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6266 (pp) REVERT: W 21 ASN cc_start: 0.8023 (t0) cc_final: 0.6965 (t0) REVERT: X 43 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7585 (mtpt) REVERT: X 117 ARG cc_start: 0.6854 (tpp80) cc_final: 0.6358 (mtt-85) REVERT: Y 29 LYS cc_start: 0.7631 (ttpt) cc_final: 0.7308 (ttmt) REVERT: Y 37 LYS cc_start: 0.6456 (tptt) cc_final: 0.6242 (mmmt) REVERT: Y 135 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8294 (mtpt) REVERT: Y 138 LYS cc_start: 0.8105 (mttt) cc_final: 0.7778 (mtpt) REVERT: Z 8 ARG cc_start: 0.6821 (mtt-85) cc_final: 0.6147 (mmm160) REVERT: Z 17 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7637 (mt) REVERT: Z 22 GLN cc_start: 0.8324 (pt0) cc_final: 0.7821 (pt0) REVERT: Z 25 ILE cc_start: 0.8410 (mp) cc_final: 0.8132 (mm) REVERT: Z 47 MET cc_start: 0.7494 (tpp) cc_final: 0.7143 (ttm) REVERT: Z 68 LYS cc_start: 0.7567 (tttt) cc_final: 0.7338 (tttm) REVERT: Z 101 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.5955 (ttmt) REVERT: a 64 ASN cc_start: 0.6382 (m-40) cc_final: 0.5978 (m-40) REVERT: a 88 LEU cc_start: 0.7514 (mt) cc_final: 0.7293 (mp) REVERT: b 38 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7294 (mmtt) REVERT: b 42 ARG cc_start: 0.7003 (mtm110) cc_final: 0.6731 (mtm110) REVERT: b 59 PHE cc_start: 0.7230 (m-80) cc_final: 0.6969 (m-80) REVERT: b 85 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7180 (ttm-80) REVERT: b 86 ASN cc_start: 0.8516 (p0) cc_final: 0.8276 (p0) REVERT: c 34 ASP cc_start: 0.7358 (m-30) cc_final: 0.7082 (m-30) REVERT: c 45 THR cc_start: 0.8402 (m) cc_final: 0.8111 (t) REVERT: c 75 GLU cc_start: 0.4426 (tp30) cc_final: 0.4131 (tp30) REVERT: d 43 ILE cc_start: 0.7893 (tp) cc_final: 0.7654 (tp) REVERT: e 13 LYS cc_start: 0.8489 (mttm) cc_final: 0.8043 (mtpt) REVERT: e 38 MET cc_start: 0.8000 (ttt) cc_final: 0.7581 (ttm) REVERT: f 125 LYS cc_start: 0.6435 (mttt) cc_final: 0.6098 (mmtt) REVERT: h 4 GLN cc_start: 0.3314 (tt0) cc_final: 0.2716 (tp40) REVERT: h 5 MET cc_start: 0.5118 (mmp) cc_final: 0.4401 (mmm) REVERT: h 17 TRP cc_start: 0.5841 (OUTLIER) cc_final: 0.2471 (p-90) REVERT: h 26 GLN cc_start: 0.7402 (mm110) cc_final: 0.5693 (tp40) REVERT: h 119 GLN cc_start: 0.6659 (mm-40) cc_final: 0.6244 (mm110) REVERT: h 207 CYS cc_start: 0.5496 (OUTLIER) cc_final: 0.4870 (p) REVERT: h 215 GLN cc_start: 0.5857 (mm110) cc_final: 0.4687 (mm110) REVERT: h 231 ASP cc_start: 0.7461 (p0) cc_final: 0.7225 (t0) REVERT: h 272 GLN cc_start: 0.4531 (pm20) cc_final: 0.3281 (tp-100) REVERT: h 285 GLN cc_start: 0.7082 (pt0) cc_final: 0.6427 (mt0) REVERT: h 286 CYS cc_start: 0.7844 (t) cc_final: 0.7387 (t) REVERT: h 287 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7296 (p) outliers start: 157 outliers final: 87 residues processed: 1093 average time/residue: 0.8339 time to fit residues: 1495.3469 Evaluate side-chains 992 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 891 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain N residue 106 CYS Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 CYS Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 82 ASN Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 101 LYS Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 26 GLN Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 207 CYS Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 260 ASP Chi-restraints excluded: chain h residue 287 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 6.9990 chunk 362 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 475 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 544 optimal weight: 0.9980 chunk 440 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 325 optimal weight: 10.0000 chunk 572 optimal weight: 0.7980 chunk 160 optimal weight: 20.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 155 HIS C 92 GLN C 202 GLN D 113 GLN E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 224 ASN G 137 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN J 7 ASN J 116 HIS ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS P 26 ASN P 32 HIS R 8 GLN T 72 GLN T 105 ASN U 85 ASN Y 46 HIS ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN Z 106 GLN a 112 ASN b 25 ASN c 19 HIS ** d 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 131 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 84823 Z= 0.412 Angle : 0.748 11.014 123619 Z= 0.376 Chirality : 0.044 0.490 15363 Planarity : 0.006 0.076 8630 Dihedral : 24.020 179.976 35074 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.97 % Rotamer: Outliers : 5.63 % Allowed : 16.63 % Favored : 77.74 % 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: -1.05 (0.12), residues: 4788 helix: 0.53 (0.13), residues: 1570 sheet: -1.33 (0.17), residues: 867 loop : -1.25 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP h 17 HIS 0.010 0.002 HIS Q 79 PHE 0.037 0.003 PHE F 47 TYR 0.022 0.003 TYR E 107 ARG 0.010 0.001 ARG B 102 *********************** 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 1122 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 886 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.7701 (tttt) cc_final: 0.7273 (ttpt) REVERT: B 69 GLU cc_start: 0.7872 (tt0) cc_final: 0.7240 (tp30) REVERT: B 75 SER cc_start: 0.9027 (t) cc_final: 0.8679 (m) REVERT: B 109 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.7932 (p) REVERT: B 181 GLU cc_start: 0.6878 (tp30) cc_final: 0.6622 (tp30) REVERT: B 192 GLU cc_start: 0.5964 (mm-30) cc_final: 0.5436 (mp0) REVERT: C 95 ASN cc_start: 0.7761 (t0) cc_final: 0.7420 (t0) REVERT: C 99 ASN cc_start: 0.8626 (t0) cc_final: 0.8170 (t0) REVERT: C 122 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8220 (mt-10) REVERT: C 144 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7334 (tttm) REVERT: C 177 GLN cc_start: 0.7443 (mt0) cc_final: 0.7223 (mt0) REVERT: C 181 LEU cc_start: 0.5685 (tp) cc_final: 0.5397 (tt) REVERT: C 182 LYS cc_start: 0.7380 (tmtt) cc_final: 0.7078 (ttmt) REVERT: C 207 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7524 (pp) REVERT: C 230 GLU cc_start: 0.7347 (tt0) cc_final: 0.6961 (tp30) REVERT: D 120 GLN cc_start: 0.8768 (mp10) cc_final: 0.8460 (mp10) REVERT: D 121 ARG cc_start: 0.7411 (tpm-80) cc_final: 0.7060 (ttm-80) REVERT: D 144 SER cc_start: 0.8174 (t) cc_final: 0.7724 (m) REVERT: D 161 SER cc_start: 0.8922 (t) cc_final: 0.8440 (p) REVERT: D 190 SER cc_start: 0.7860 (t) cc_final: 0.7598 (p) REVERT: D 215 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6823 (mt) REVERT: E 31 GLU cc_start: 0.7106 (pm20) cc_final: 0.6535 (pm20) REVERT: E 74 GLN cc_start: 0.7830 (tt0) cc_final: 0.7518 (mt0) REVERT: E 83 SER cc_start: 0.6976 (t) cc_final: 0.6515 (m) REVERT: E 85 GLU cc_start: 0.6821 (pt0) cc_final: 0.6581 (pt0) REVERT: E 87 TYR cc_start: 0.5990 (m-80) cc_final: 0.5036 (m-80) REVERT: E 89 GLU cc_start: 0.5701 (mt-10) cc_final: 0.5261 (tt0) REVERT: E 117 ARG cc_start: 0.7341 (tpt-90) cc_final: 0.6567 (ttm110) REVERT: E 120 TYR cc_start: 0.8099 (m-80) cc_final: 0.6599 (t80) REVERT: E 125 PHE cc_start: 0.7380 (t80) cc_final: 0.7063 (t80) REVERT: E 146 ARG cc_start: 0.7515 (tpp80) cc_final: 0.5819 (ptm160) REVERT: F 7 LYS cc_start: 0.8078 (mttt) cc_final: 0.7810 (mtmt) REVERT: F 32 SER cc_start: 0.8694 (t) cc_final: 0.8395 (p) REVERT: F 39 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7441 (mtp-110) REVERT: F 79 ASP cc_start: 0.7523 (t0) cc_final: 0.6830 (t70) REVERT: F 97 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6273 (mm-30) REVERT: F 118 GLU cc_start: 0.6300 (mm-30) cc_final: 0.6036 (tp30) REVERT: F 163 ASP cc_start: 0.7123 (t0) cc_final: 0.6756 (t0) REVERT: F 205 PHE cc_start: 0.7445 (m-80) cc_final: 0.7058 (m-10) REVERT: F 221 ARG cc_start: 0.7682 (ttm170) cc_final: 0.6901 (mtt180) REVERT: F 255 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6816 (ptm-80) REVERT: G 37 ASP cc_start: 0.8231 (t70) cc_final: 0.7853 (m-30) REVERT: G 56 TYR cc_start: 0.8374 (m-80) cc_final: 0.8061 (m-80) REVERT: G 160 GLU cc_start: 0.7442 (tt0) cc_final: 0.7120 (tt0) REVERT: G 191 LYS cc_start: 0.7035 (tttt) cc_final: 0.6818 (ttmt) REVERT: H 12 CYS cc_start: 0.6405 (t) cc_final: 0.5806 (m) REVERT: H 44 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6920 (tt0) REVERT: H 56 ASN cc_start: 0.8626 (m110) cc_final: 0.8410 (m-40) REVERT: H 89 THR cc_start: 0.8687 (m) cc_final: 0.8423 (p) REVERT: H 131 ARG cc_start: 0.5535 (mpt90) cc_final: 0.4572 (mtm110) REVERT: H 154 ARG cc_start: 0.6404 (mpt-90) cc_final: 0.5976 (mpp80) REVERT: H 200 LYS cc_start: 0.7264 (tttt) cc_final: 0.6656 (mptt) REVERT: H 203 LYS cc_start: 0.7553 (tttt) cc_final: 0.7019 (ptmt) REVERT: H 217 MET cc_start: 0.6192 (tpp) cc_final: 0.5581 (mmp) REVERT: I 15 LYS cc_start: 0.6450 (mttm) cc_final: 0.6226 (mptt) REVERT: I 57 ARG cc_start: 0.4526 (mmm-85) cc_final: 0.4118 (mmp80) REVERT: I 61 ILE cc_start: 0.5384 (pt) cc_final: 0.5032 (mp) REVERT: I 99 ARG cc_start: 0.6546 (ttt180) cc_final: 0.6111 (tpt170) REVERT: I 107 LYS cc_start: 0.5705 (mttt) cc_final: 0.5202 (pttm) REVERT: I 163 GLN cc_start: 0.6671 (tt0) cc_final: 0.5911 (tm-30) REVERT: J 64 ASN cc_start: 0.7024 (t0) cc_final: 0.6668 (t0) REVERT: J 77 ARG cc_start: 0.7031 (ttp-170) cc_final: 0.6354 (ttm170) REVERT: J 83 TYR cc_start: 0.8002 (t80) cc_final: 0.7419 (t80) REVERT: J 92 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.6947 (ttp80) REVERT: J 95 THR cc_start: 0.8400 (m) cc_final: 0.8036 (p) REVERT: J 144 LYS cc_start: 0.6764 (ptpt) cc_final: 0.6105 (mmtt) REVERT: J 167 GLN cc_start: 0.6481 (tt0) cc_final: 0.6110 (tp40) REVERT: K 17 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6659 (ttm-80) REVERT: K 18 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7654 (mmt180) REVERT: K 92 MET cc_start: 0.7846 (ttt) cc_final: 0.7538 (ttm) REVERT: K 101 LYS cc_start: 0.7495 (ptmt) cc_final: 0.7051 (mmmt) REVERT: K 138 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6939 (mtt-85) REVERT: L 26 ASP cc_start: 0.8078 (t0) cc_final: 0.7565 (t0) REVERT: L 29 MET cc_start: 0.7047 (ttm) cc_final: 0.6789 (ttm) REVERT: M 45 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7863 (mtpt) REVERT: M 97 ARG cc_start: 0.7485 (ptt90) cc_final: 0.6727 (ttt90) REVERT: N 102 LYS cc_start: 0.4651 (ttpt) cc_final: 0.4265 (mmmt) REVERT: O 13 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7821 (pt0) REVERT: O 19 ARG cc_start: 0.7174 (ppt170) cc_final: 0.6777 (mtm180) REVERT: O 27 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.6032 (mmtp) REVERT: O 42 LYS cc_start: 0.6959 (mmmt) cc_final: 0.6714 (mmmm) REVERT: O 106 ARG cc_start: 0.7869 (mmt90) cc_final: 0.7163 (ttp-110) REVERT: P 63 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7643 (ptpp) REVERT: P 75 MET cc_start: 0.7550 (ttp) cc_final: 0.7245 (tmm) REVERT: P 80 ASP cc_start: 0.8149 (t0) cc_final: 0.7882 (t0) REVERT: P 107 THR cc_start: 0.7952 (m) cc_final: 0.7695 (t) REVERT: P 143 LYS cc_start: 0.8149 (tmmt) cc_final: 0.7424 (tttp) REVERT: Q 34 MET cc_start: 0.7825 (mtt) cc_final: 0.7086 (mtp) REVERT: Q 35 GLN cc_start: 0.8148 (mt0) cc_final: 0.7340 (mp10) REVERT: Q 106 GLU cc_start: 0.6569 (pt0) cc_final: 0.5992 (tm-30) REVERT: Q 108 LYS cc_start: 0.7298 (ptpt) cc_final: 0.6831 (mmtm) REVERT: Q 111 MET cc_start: 0.7249 (mmt) cc_final: 0.6001 (mtt) REVERT: R 43 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7171 (mp0) REVERT: S 62 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7295 (mt0) REVERT: S 67 ARG cc_start: 0.6288 (mtp85) cc_final: 0.6010 (ttp80) REVERT: S 76 GLU cc_start: 0.4033 (tp30) cc_final: 0.3532 (tp30) REVERT: S 81 ARG cc_start: 0.7128 (tmm-80) cc_final: 0.6922 (ttp-170) REVERT: S 89 SER cc_start: 0.5584 (p) cc_final: 0.5355 (p) REVERT: S 92 ASP cc_start: 0.6673 (m-30) cc_final: 0.6424 (m-30) REVERT: S 97 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6028 (mm-30) REVERT: S 118 GLN cc_start: 0.5961 (tp-100) cc_final: 0.5188 (pt0) REVERT: T 21 ASP cc_start: 0.8077 (t0) cc_final: 0.7651 (t0) REVERT: T 24 ARG cc_start: 0.6952 (mtp85) cc_final: 0.6582 (mtm-85) REVERT: T 63 GLU cc_start: 0.7246 (tt0) cc_final: 0.6652 (tp30) REVERT: T 78 LYS cc_start: 0.7619 (ttmt) cc_final: 0.7116 (tptt) REVERT: T 91 LYS cc_start: 0.7898 (mttm) cc_final: 0.7209 (mmmt) REVERT: T 112 GLU cc_start: 0.7677 (tt0) cc_final: 0.6755 (tm-30) REVERT: T 127 TRP cc_start: 0.7850 (m-10) cc_final: 0.7608 (m-10) REVERT: U 27 LYS cc_start: 0.7557 (ptpp) cc_final: 0.7221 (ptpt) REVERT: U 88 MET cc_start: 0.8520 (mtm) cc_final: 0.8295 (mtp) REVERT: U 137 GLN cc_start: 0.7772 (mt0) cc_final: 0.7486 (mt0) REVERT: V 19 ARG cc_start: 0.4421 (mpt180) cc_final: 0.3470 (ttm170) REVERT: V 83 ARG cc_start: 0.7620 (mmt90) cc_final: 0.7378 (mpt-90) REVERT: W 11 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7234 (pp) REVERT: W 21 ASN cc_start: 0.8261 (t0) cc_final: 0.7378 (t0) REVERT: W 45 ARG cc_start: 0.6649 (mtt180) cc_final: 0.6236 (mtp180) REVERT: X 41 MET cc_start: 0.7480 (mtm) cc_final: 0.7134 (mtm) REVERT: X 117 ARG cc_start: 0.7042 (tpp80) cc_final: 0.6504 (mtt-85) REVERT: Y 29 LYS cc_start: 0.7489 (ttpt) cc_final: 0.7136 (ttmt) REVERT: Y 37 LYS cc_start: 0.6571 (tptt) cc_final: 0.6334 (mmmt) REVERT: Y 119 ARG cc_start: 0.6683 (mtm-85) cc_final: 0.6292 (mtp85) REVERT: Y 138 LYS cc_start: 0.8186 (mttt) cc_final: 0.7843 (mtpt) REVERT: Z 8 ARG cc_start: 0.6632 (mtt-85) cc_final: 0.6017 (mmm160) REVERT: Z 17 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7773 (pp) REVERT: Z 22 GLN cc_start: 0.8433 (pt0) cc_final: 0.8023 (pt0) REVERT: Z 47 MET cc_start: 0.7628 (tpp) cc_final: 0.7264 (ttm) REVERT: Z 68 LYS cc_start: 0.7910 (tttt) cc_final: 0.7702 (tttm) REVERT: Z 96 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6930 (pp) REVERT: Z 101 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.5897 (ttmt) REVERT: a 64 ASN cc_start: 0.6606 (m-40) cc_final: 0.6222 (m-40) REVERT: b 38 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7423 (mmtt) REVERT: c 34 ASP cc_start: 0.7490 (m-30) cc_final: 0.7131 (m-30) REVERT: c 45 THR cc_start: 0.8510 (m) cc_final: 0.8171 (t) REVERT: c 75 GLU cc_start: 0.4625 (tp30) cc_final: 0.4239 (tp30) REVERT: e 13 LYS cc_start: 0.8430 (mttm) cc_final: 0.7969 (mtpt) REVERT: e 31 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8123 (mm) REVERT: e 38 MET cc_start: 0.8588 (ttt) cc_final: 0.8020 (ttm) REVERT: f 125 LYS cc_start: 0.6487 (mttt) cc_final: 0.6117 (mmtt) REVERT: h 4 GLN cc_start: 0.3452 (tt0) cc_final: 0.2657 (tp40) REVERT: h 5 MET cc_start: 0.5428 (mmp) cc_final: 0.4266 (mmm) REVERT: h 17 TRP cc_start: 0.5896 (OUTLIER) cc_final: 0.3130 (p-90) REVERT: h 26 GLN cc_start: 0.7090 (mm110) cc_final: 0.5761 (tp40) REVERT: h 207 CYS cc_start: 0.5795 (OUTLIER) cc_final: 0.4929 (p) REVERT: h 257 LYS cc_start: 0.6449 (ttmp) cc_final: 0.6143 (mtmt) REVERT: h 272 GLN cc_start: 0.4865 (pm20) cc_final: 0.3578 (tp-100) REVERT: h 285 GLN cc_start: 0.7340 (pt0) cc_final: 0.6618 (mt0) REVERT: h 286 CYS cc_start: 0.8138 (t) cc_final: 0.7628 (t) REVERT: h 287 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7457 (p) outliers start: 236 outliers final: 168 residues processed: 1042 average time/residue: 0.8270 time to fit residues: 1427.5364 Evaluate side-chains 1005 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 824 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 187 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 176 LYS Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain N residue 106 CYS Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 36 SER Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 CYS Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 41 ILE Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 99 LEU Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain U residue 126 GLN Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 72 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain Z residue 101 LYS Chi-restraints excluded: chain Z residue 103 SER Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 100 VAL Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 64 CYS Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 26 GLN Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 91 LYS Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 203 ASP Chi-restraints excluded: chain h residue 207 CYS Chi-restraints excluded: chain h residue 287 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 0.8980 chunk 574 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 374 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 638 optimal weight: 2.9990 chunk 530 optimal weight: 1.9990 chunk 295 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 335 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN D 172 ASN E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN J 7 ASN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS P 38 ASN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS T 105 ASN U 91 HIS V 81 GLN X 98 GLN Y 77 ASN Y 97 ASN Z 106 GLN ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 84823 Z= 0.239 Angle : 0.619 10.323 123619 Z= 0.313 Chirality : 0.039 0.492 15363 Planarity : 0.004 0.051 8630 Dihedral : 23.976 179.767 35074 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.72 % Rotamer: Outliers : 4.68 % Allowed : 18.44 % Favored : 76.88 % 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: -0.86 (0.12), residues: 4788 helix: 0.79 (0.13), residues: 1567 sheet: -1.26 (0.17), residues: 876 loop : -1.19 (0.12), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP h 17 HIS 0.023 0.001 HIS M 106 PHE 0.028 0.002 PHE S 111 TYR 0.020 0.002 TYR L 12 ARG 0.006 0.001 ARG V 62 *********************** 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 1077 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 881 time to evaluate : 5.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.7691 (tttt) cc_final: 0.7201 (ttpt) REVERT: B 69 GLU cc_start: 0.7826 (tt0) cc_final: 0.7169 (tp30) REVERT: B 75 SER cc_start: 0.8774 (t) cc_final: 0.8510 (m) REVERT: B 78 SER cc_start: 0.8911 (t) cc_final: 0.8499 (t) REVERT: B 192 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5575 (mp0) REVERT: C 89 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7353 (mm-30) REVERT: C 95 ASN cc_start: 0.7892 (t0) cc_final: 0.7612 (t0) REVERT: C 103 MET cc_start: 0.8592 (tmm) cc_final: 0.8294 (tmm) REVERT: C 122 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8213 (mt-10) REVERT: C 144 LYS cc_start: 0.8063 (ttpt) cc_final: 0.7346 (tttm) REVERT: C 182 LYS cc_start: 0.7211 (tmtt) cc_final: 0.6881 (ttmt) REVERT: C 207 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7500 (pp) REVERT: C 230 GLU cc_start: 0.7410 (tt0) cc_final: 0.6972 (tp30) REVERT: D 68 ARG cc_start: 0.7419 (tpt170) cc_final: 0.7196 (tpt170) REVERT: D 120 GLN cc_start: 0.8449 (mp10) cc_final: 0.8224 (mp10) REVERT: D 144 SER cc_start: 0.8150 (t) cc_final: 0.7667 (m) REVERT: D 161 SER cc_start: 0.8886 (t) cc_final: 0.8428 (p) REVERT: D 190 SER cc_start: 0.7890 (t) cc_final: 0.7594 (p) REVERT: D 215 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6893 (mp) REVERT: E 31 GLU cc_start: 0.7068 (pm20) cc_final: 0.6505 (pm20) REVERT: E 74 GLN cc_start: 0.7837 (tt0) cc_final: 0.7537 (mt0) REVERT: E 83 SER cc_start: 0.6869 (t) cc_final: 0.6417 (m) REVERT: E 84 VAL cc_start: 0.7147 (p) cc_final: 0.6890 (p) REVERT: E 87 TYR cc_start: 0.5995 (m-80) cc_final: 0.5003 (m-80) REVERT: E 89 GLU cc_start: 0.5704 (mt-10) cc_final: 0.5267 (tt0) REVERT: E 117 ARG cc_start: 0.7303 (tpt-90) cc_final: 0.6525 (ttm110) REVERT: E 120 TYR cc_start: 0.8207 (m-80) cc_final: 0.6584 (t80) REVERT: E 125 PHE cc_start: 0.7372 (t80) cc_final: 0.6975 (t80) REVERT: E 127 MET cc_start: 0.7107 (tpt) cc_final: 0.6878 (tpt) REVERT: E 146 ARG cc_start: 0.7531 (tpp80) cc_final: 0.5992 (ptm160) REVERT: E 169 ASP cc_start: 0.8541 (t70) cc_final: 0.8326 (t70) REVERT: F 7 LYS cc_start: 0.7997 (mttt) cc_final: 0.7726 (mtmt) REVERT: F 32 SER cc_start: 0.8514 (t) cc_final: 0.8250 (p) REVERT: F 39 ARG cc_start: 0.8055 (mtt-85) cc_final: 0.7523 (mtp-110) REVERT: F 79 ASP cc_start: 0.7496 (t0) cc_final: 0.6791 (t70) REVERT: F 97 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6420 (mm-30) REVERT: F 118 GLU cc_start: 0.6283 (mm-30) cc_final: 0.6014 (tp30) REVERT: F 163 ASP cc_start: 0.7143 (t0) cc_final: 0.6822 (t0) REVERT: F 205 PHE cc_start: 0.7404 (m-80) cc_final: 0.7118 (m-10) REVERT: F 221 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7009 (mtt180) REVERT: F 255 ARG cc_start: 0.7178 (ttp80) cc_final: 0.6860 (ptm-80) REVERT: G 37 ASP cc_start: 0.8241 (t70) cc_final: 0.7899 (m-30) REVERT: G 56 TYR cc_start: 0.8296 (m-80) cc_final: 0.7944 (m-80) REVERT: G 160 GLU cc_start: 0.7384 (tt0) cc_final: 0.7076 (tt0) REVERT: H 12 CYS cc_start: 0.6113 (t) cc_final: 0.5592 (m) REVERT: H 44 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6921 (tt0) REVERT: H 56 ASN cc_start: 0.8618 (m110) cc_final: 0.8411 (m-40) REVERT: H 89 THR cc_start: 0.8693 (m) cc_final: 0.8432 (p) REVERT: H 131 ARG cc_start: 0.5777 (mpt90) cc_final: 0.4567 (mtm110) REVERT: H 154 ARG cc_start: 0.6291 (mpt-90) cc_final: 0.5870 (mpp80) REVERT: H 190 ARG cc_start: 0.6650 (tpt-90) cc_final: 0.6447 (tpt90) REVERT: H 200 LYS cc_start: 0.7264 (tttt) cc_final: 0.6648 (mptt) REVERT: H 203 LYS cc_start: 0.7579 (tttt) cc_final: 0.7054 (ptmt) REVERT: H 217 MET cc_start: 0.6182 (tpp) cc_final: 0.5586 (mmp) REVERT: I 15 LYS cc_start: 0.6357 (mttm) cc_final: 0.6157 (mptt) REVERT: I 57 ARG cc_start: 0.4618 (mmm-85) cc_final: 0.4204 (mmp80) REVERT: I 61 ILE cc_start: 0.5044 (pt) cc_final: 0.4802 (mp) REVERT: I 99 ARG cc_start: 0.6548 (ttt180) cc_final: 0.6154 (tpt170) REVERT: I 107 LYS cc_start: 0.5743 (mttt) cc_final: 0.5231 (pttt) REVERT: I 163 GLN cc_start: 0.6682 (tt0) cc_final: 0.5978 (tm-30) REVERT: J 77 ARG cc_start: 0.7065 (ttp-170) cc_final: 0.6462 (ttm170) REVERT: J 92 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.6824 (ttp80) REVERT: J 95 THR cc_start: 0.8326 (m) cc_final: 0.8008 (p) REVERT: J 144 LYS cc_start: 0.6679 (ptpt) cc_final: 0.6022 (mmtt) REVERT: J 157 LYS cc_start: 0.6937 (tppt) cc_final: 0.6359 (mppt) REVERT: J 167 GLN cc_start: 0.6450 (tt0) cc_final: 0.6169 (tp40) REVERT: K 17 ARG cc_start: 0.7799 (ttt90) cc_final: 0.6621 (ttm-80) REVERT: K 18 ARG cc_start: 0.8131 (mtt90) cc_final: 0.7595 (mmt180) REVERT: K 34 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6511 (mp0) REVERT: K 101 LYS cc_start: 0.7514 (ptmt) cc_final: 0.7047 (mmmt) REVERT: K 138 ARG cc_start: 0.7253 (mtt180) cc_final: 0.6881 (mtt-85) REVERT: L 2 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5779 (tt) REVERT: L 26 ASP cc_start: 0.8087 (t0) cc_final: 0.7570 (t0) REVERT: M 45 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7876 (mtpt) REVERT: M 97 ARG cc_start: 0.7373 (ptt90) cc_final: 0.6638 (ttt90) REVERT: M 107 LYS cc_start: 0.7681 (mmtp) cc_final: 0.7311 (mmtt) REVERT: N 102 LYS cc_start: 0.4595 (ttpt) cc_final: 0.4228 (mmmt) REVERT: O 13 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: O 19 ARG cc_start: 0.7145 (ppt170) cc_final: 0.6732 (mtm180) REVERT: O 27 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6157 (mmtp) REVERT: O 35 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6719 (tp30) REVERT: O 42 LYS cc_start: 0.6922 (mmmt) cc_final: 0.6691 (mmmm) REVERT: O 106 ARG cc_start: 0.7899 (mmt90) cc_final: 0.7160 (ttp-110) REVERT: P 38 ASN cc_start: 0.7174 (m-40) cc_final: 0.6830 (m110) REVERT: P 75 MET cc_start: 0.7706 (ttp) cc_final: 0.7359 (tmm) REVERT: P 80 ASP cc_start: 0.8164 (t0) cc_final: 0.7877 (t0) REVERT: P 107 THR cc_start: 0.7876 (m) cc_final: 0.7625 (t) REVERT: P 130 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7464 (tm-30) REVERT: P 143 LYS cc_start: 0.8107 (tmmt) cc_final: 0.7507 (tppt) REVERT: Q 34 MET cc_start: 0.7801 (mtt) cc_final: 0.7017 (mtp) REVERT: Q 35 GLN cc_start: 0.8103 (mt0) cc_final: 0.7280 (mp10) REVERT: Q 106 GLU cc_start: 0.6301 (pt0) cc_final: 0.5788 (tm-30) REVERT: Q 108 LYS cc_start: 0.7265 (ptpt) cc_final: 0.6823 (mmtm) REVERT: Q 111 MET cc_start: 0.7275 (mmt) cc_final: 0.5984 (mtt) REVERT: R 43 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7121 (mp0) REVERT: R 102 GLU cc_start: 0.7672 (tt0) cc_final: 0.7201 (tp30) REVERT: S 62 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7326 (mt0) REVERT: S 67 ARG cc_start: 0.6218 (mtp85) cc_final: 0.5930 (ttp80) REVERT: S 81 ARG cc_start: 0.6894 (tmm-80) cc_final: 0.6622 (ttp-170) REVERT: S 89 SER cc_start: 0.5416 (p) cc_final: 0.5145 (p) REVERT: S 92 ASP cc_start: 0.6705 (m-30) cc_final: 0.6424 (m-30) REVERT: S 97 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6614 (mm-30) REVERT: T 21 ASP cc_start: 0.8104 (t0) cc_final: 0.7649 (t0) REVERT: T 24 ARG cc_start: 0.7018 (mtp85) cc_final: 0.6635 (mtm-85) REVERT: T 63 GLU cc_start: 0.7223 (tt0) cc_final: 0.6544 (tp30) REVERT: T 78 LYS cc_start: 0.7627 (ttmt) cc_final: 0.7129 (tptt) REVERT: T 91 LYS cc_start: 0.8018 (mttm) cc_final: 0.7299 (mmmt) REVERT: T 112 GLU cc_start: 0.7630 (tt0) cc_final: 0.6730 (tm-30) REVERT: T 127 TRP cc_start: 0.7752 (m-10) cc_final: 0.7501 (m-10) REVERT: U 27 LYS cc_start: 0.7701 (ptpp) cc_final: 0.7177 (mtmt) REVERT: U 98 SER cc_start: 0.8684 (t) cc_final: 0.7926 (p) REVERT: U 116 ASP cc_start: 0.7125 (t0) cc_final: 0.6806 (t0) REVERT: U 137 GLN cc_start: 0.7768 (mt0) cc_final: 0.7436 (mt0) REVERT: V 19 ARG cc_start: 0.4431 (mpt180) cc_final: 0.3482 (ptm160) REVERT: W 11 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.6871 (pp) REVERT: W 21 ASN cc_start: 0.8244 (t0) cc_final: 0.7221 (t0) REVERT: X 41 MET cc_start: 0.7469 (mtm) cc_final: 0.7026 (mtm) REVERT: X 51 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7676 (pp20) REVERT: X 117 ARG cc_start: 0.6995 (tpp80) cc_final: 0.6437 (mtt-85) REVERT: Y 37 LYS cc_start: 0.6553 (tptt) cc_final: 0.6294 (mmmt) REVERT: Y 138 LYS cc_start: 0.8227 (mttt) cc_final: 0.7845 (mtpt) REVERT: Z 8 ARG cc_start: 0.6644 (mtt-85) cc_final: 0.6045 (mmm160) REVERT: Z 17 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7828 (pp) REVERT: Z 22 GLN cc_start: 0.8397 (pt0) cc_final: 0.7869 (pt0) REVERT: Z 47 MET cc_start: 0.7590 (tpp) cc_final: 0.7253 (ttm) REVERT: Z 68 LYS cc_start: 0.7871 (tttt) cc_final: 0.7650 (tttm) REVERT: Z 96 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7050 (pp) REVERT: Z 101 LYS cc_start: 0.6478 (OUTLIER) cc_final: 0.5908 (ttmt) REVERT: a 60 LYS cc_start: 0.7480 (tppt) cc_final: 0.7124 (ttmt) REVERT: a 64 ASN cc_start: 0.6497 (m-40) cc_final: 0.6150 (m-40) REVERT: b 38 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7343 (mmtt) REVERT: c 34 ASP cc_start: 0.7492 (m-30) cc_final: 0.7130 (m-30) REVERT: c 45 THR cc_start: 0.8208 (m) cc_final: 0.7890 (t) REVERT: c 75 GLU cc_start: 0.4664 (tp30) cc_final: 0.4279 (tp30) REVERT: e 13 LYS cc_start: 0.8385 (mttm) cc_final: 0.7859 (mtpt) REVERT: e 38 MET cc_start: 0.8355 (ttt) cc_final: 0.7810 (ttm) REVERT: f 125 LYS cc_start: 0.6391 (mttt) cc_final: 0.6064 (mmtt) REVERT: g 132 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.5369 (ttt) REVERT: h 4 GLN cc_start: 0.3730 (tt0) cc_final: 0.2897 (tp40) REVERT: h 5 MET cc_start: 0.5273 (mmp) cc_final: 0.4283 (mmm) REVERT: h 17 TRP cc_start: 0.5924 (OUTLIER) cc_final: 0.2969 (p-90) REVERT: h 149 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.5973 (mp0) REVERT: h 207 CYS cc_start: 0.5823 (OUTLIER) cc_final: 0.5020 (p) REVERT: h 225 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6787 (ttmt) REVERT: h 257 LYS cc_start: 0.6387 (ttmp) cc_final: 0.6181 (mtmt) REVERT: h 272 GLN cc_start: 0.4867 (pm20) cc_final: 0.3532 (tp-100) REVERT: h 285 GLN cc_start: 0.7224 (pt0) cc_final: 0.6485 (mt0) REVERT: h 286 CYS cc_start: 0.7948 (t) cc_final: 0.7517 (t) REVERT: h 287 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7401 (p) outliers start: 196 outliers final: 143 residues processed: 1003 average time/residue: 0.8260 time to fit residues: 1374.5712 Evaluate side-chains 1004 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 845 time to evaluate : 4.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 20 PHE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 106 HIS Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain N residue 106 CYS Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 CYS Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 11 HIS Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 34 MET Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain X residue 27 ILE Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain Z residue 101 LYS Chi-restraints excluded: chain Z residue 103 SER Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 26 GLN Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 91 LYS Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain g residue 132 MET Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 160 SER Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 203 ASP Chi-restraints excluded: chain h residue 207 CYS Chi-restraints excluded: chain h residue 225 LYS Chi-restraints excluded: chain h residue 287 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 466 optimal weight: 0.9980 chunk 361 optimal weight: 3.9990 chunk 537 optimal weight: 4.9990 chunk 356 optimal weight: 0.9980 chunk 636 optimal weight: 10.0000 chunk 398 optimal weight: 2.9990 chunk 387 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN K 156 HIS ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN Y 77 ASN Y 97 ASN Z 106 GLN ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 159 ASN h 162 ASN h 226 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 84823 Z= 0.228 Angle : 0.607 10.554 123619 Z= 0.307 Chirality : 0.038 0.475 15363 Planarity : 0.004 0.052 8630 Dihedral : 23.919 179.732 35070 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 5.06 % Allowed : 18.63 % Favored : 76.31 % 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: -0.74 (0.12), residues: 4788 helix: 0.87 (0.13), residues: 1574 sheet: -1.14 (0.17), residues: 882 loop : -1.15 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP h 17 HIS 0.016 0.001 HIS T 11 PHE 0.027 0.002 PHE S 111 TYR 0.019 0.002 TYR L 12 ARG 0.008 0.001 ARG f 81 *********************** 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 1083 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 871 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 LYS cc_start: 0.7237 (ttmt) cc_final: 0.6937 (ttpt) REVERT: B 52 LYS cc_start: 0.7683 (tttt) cc_final: 0.7167 (ttpt) REVERT: B 59 LEU cc_start: 0.7446 (mt) cc_final: 0.7236 (mp) REVERT: B 69 GLU cc_start: 0.7789 (tt0) cc_final: 0.7173 (tp30) REVERT: B 75 SER cc_start: 0.8798 (t) cc_final: 0.8538 (m) REVERT: B 78 SER cc_start: 0.8877 (t) cc_final: 0.8462 (t) REVERT: B 181 GLU cc_start: 0.7057 (tp30) cc_final: 0.6661 (tp30) REVERT: B 192 GLU cc_start: 0.6179 (mm-30) cc_final: 0.5623 (mp0) REVERT: C 42 ARG cc_start: 0.6911 (mmm-85) cc_final: 0.6590 (mmm160) REVERT: C 89 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7374 (mm-30) REVERT: C 95 ASN cc_start: 0.7897 (t0) cc_final: 0.7634 (t0) REVERT: C 103 MET cc_start: 0.8618 (tmm) cc_final: 0.8305 (tmm) REVERT: C 122 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8216 (mt-10) REVERT: C 144 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7338 (tttm) REVERT: C 182 LYS cc_start: 0.7193 (tmtt) cc_final: 0.6884 (ttmt) REVERT: C 207 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7498 (pp) REVERT: C 230 GLU cc_start: 0.7440 (tt0) cc_final: 0.6983 (tp30) REVERT: D 68 ARG cc_start: 0.7450 (tpt170) cc_final: 0.7199 (tpt170) REVERT: D 120 GLN cc_start: 0.8491 (mp10) cc_final: 0.8229 (mp10) REVERT: D 144 SER cc_start: 0.8133 (t) cc_final: 0.7655 (m) REVERT: D 161 SER cc_start: 0.8880 (t) cc_final: 0.8403 (p) REVERT: D 190 SER cc_start: 0.7853 (t) cc_final: 0.7586 (p) REVERT: D 215 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6875 (mp) REVERT: E 1 MET cc_start: 0.5208 (ttt) cc_final: 0.4480 (ptp) REVERT: E 31 GLU cc_start: 0.7049 (pm20) cc_final: 0.6473 (pm20) REVERT: E 32 ASP cc_start: 0.6250 (m-30) cc_final: 0.5906 (m-30) REVERT: E 74 GLN cc_start: 0.7897 (tt0) cc_final: 0.7591 (mt0) REVERT: E 83 SER cc_start: 0.6851 (t) cc_final: 0.6400 (m) REVERT: E 84 VAL cc_start: 0.7188 (p) cc_final: 0.6971 (p) REVERT: E 87 TYR cc_start: 0.6316 (m-80) cc_final: 0.5651 (m-80) REVERT: E 89 GLU cc_start: 0.5689 (mt-10) cc_final: 0.5308 (tt0) REVERT: E 117 ARG cc_start: 0.7291 (tpt-90) cc_final: 0.6507 (ttm110) REVERT: E 120 TYR cc_start: 0.8220 (m-80) cc_final: 0.6501 (t80) REVERT: E 125 PHE cc_start: 0.7400 (t80) cc_final: 0.7017 (t80) REVERT: E 127 MET cc_start: 0.7104 (tpt) cc_final: 0.6862 (tpt) REVERT: E 146 ARG cc_start: 0.7565 (tpp80) cc_final: 0.5887 (ptm160) REVERT: E 169 ASP cc_start: 0.8469 (t70) cc_final: 0.8201 (t70) REVERT: F 7 LYS cc_start: 0.7958 (mttt) cc_final: 0.7674 (mtmt) REVERT: F 32 SER cc_start: 0.8563 (t) cc_final: 0.8335 (p) REVERT: F 39 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7529 (mtp-110) REVERT: F 79 ASP cc_start: 0.7580 (t0) cc_final: 0.6855 (t70) REVERT: F 97 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6427 (mm-30) REVERT: F 118 GLU cc_start: 0.6283 (mm-30) cc_final: 0.6022 (tp30) REVERT: F 163 ASP cc_start: 0.7265 (t0) cc_final: 0.6913 (t0) REVERT: F 255 ARG cc_start: 0.7235 (ttp80) cc_final: 0.6880 (ptm-80) REVERT: G 37 ASP cc_start: 0.8119 (t70) cc_final: 0.7867 (m-30) REVERT: G 56 TYR cc_start: 0.8177 (m-80) cc_final: 0.7874 (m-80) REVERT: G 160 GLU cc_start: 0.7374 (tt0) cc_final: 0.7059 (tt0) REVERT: H 12 CYS cc_start: 0.6091 (t) cc_final: 0.5582 (m) REVERT: H 44 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6927 (tt0) REVERT: H 56 ASN cc_start: 0.8604 (m110) cc_final: 0.8396 (m-40) REVERT: H 89 THR cc_start: 0.8689 (m) cc_final: 0.8464 (p) REVERT: H 131 ARG cc_start: 0.5736 (mpt90) cc_final: 0.4495 (mtm110) REVERT: H 154 ARG cc_start: 0.6306 (mpt-90) cc_final: 0.5870 (mpp80) REVERT: H 200 LYS cc_start: 0.7254 (tttt) cc_final: 0.6625 (mptt) REVERT: H 203 LYS cc_start: 0.7578 (tttt) cc_final: 0.7056 (ptmt) REVERT: H 217 MET cc_start: 0.5962 (tpp) cc_final: 0.5557 (mmp) REVERT: I 15 LYS cc_start: 0.6366 (mttm) cc_final: 0.6159 (mptt) REVERT: I 57 ARG cc_start: 0.4619 (mmm-85) cc_final: 0.4205 (mmp80) REVERT: I 61 ILE cc_start: 0.5136 (pt) cc_final: 0.4905 (mp) REVERT: I 107 LYS cc_start: 0.5549 (mttt) cc_final: 0.5089 (pttt) REVERT: I 163 GLN cc_start: 0.6685 (tt0) cc_final: 0.5978 (tm-30) REVERT: J 37 LYS cc_start: 0.7662 (mmmm) cc_final: 0.6997 (mptt) REVERT: J 77 ARG cc_start: 0.7055 (ttp-170) cc_final: 0.6456 (ttm170) REVERT: J 92 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.6879 (ttp80) REVERT: J 95 THR cc_start: 0.8318 (m) cc_final: 0.8007 (p) REVERT: J 144 LYS cc_start: 0.6619 (ptpt) cc_final: 0.6037 (mmtt) REVERT: J 157 LYS cc_start: 0.6901 (tppt) cc_final: 0.6210 (mmtm) REVERT: J 167 GLN cc_start: 0.6383 (tt0) cc_final: 0.6089 (tp40) REVERT: K 17 ARG cc_start: 0.7801 (ttt90) cc_final: 0.6631 (ttm-80) REVERT: K 18 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7620 (mmt180) REVERT: K 34 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6308 (mp0) REVERT: K 101 LYS cc_start: 0.7465 (ptmt) cc_final: 0.7090 (mmmt) REVERT: K 138 ARG cc_start: 0.7269 (mtt180) cc_final: 0.6903 (mtt-85) REVERT: L 2 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5900 (tt) REVERT: L 26 ASP cc_start: 0.8186 (t0) cc_final: 0.7735 (t0) REVERT: M 45 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7889 (mtpt) REVERT: M 97 ARG cc_start: 0.7315 (ptt90) cc_final: 0.6618 (ttt90) REVERT: N 102 LYS cc_start: 0.4698 (ttpt) cc_final: 0.4343 (mmmt) REVERT: O 13 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7923 (pt0) REVERT: O 19 ARG cc_start: 0.7126 (ppt170) cc_final: 0.6735 (mtm180) REVERT: O 27 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6164 (mmtp) REVERT: O 35 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6736 (tp30) REVERT: O 106 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7112 (ttp-110) REVERT: P 75 MET cc_start: 0.7710 (ttp) cc_final: 0.7379 (tmm) REVERT: P 80 ASP cc_start: 0.8169 (t0) cc_final: 0.7870 (t0) REVERT: P 107 THR cc_start: 0.7860 (m) cc_final: 0.7626 (t) REVERT: P 143 LYS cc_start: 0.8127 (tmmt) cc_final: 0.7513 (tppt) REVERT: Q 34 MET cc_start: 0.7824 (mtt) cc_final: 0.7055 (mtp) REVERT: Q 35 GLN cc_start: 0.8118 (mt0) cc_final: 0.7242 (mp10) REVERT: Q 106 GLU cc_start: 0.6485 (pt0) cc_final: 0.6016 (tt0) REVERT: Q 108 LYS cc_start: 0.7064 (ptpt) cc_final: 0.6774 (mmtm) REVERT: Q 111 MET cc_start: 0.7256 (mmt) cc_final: 0.6072 (mtt) REVERT: R 43 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7061 (mp0) REVERT: R 102 GLU cc_start: 0.7657 (tt0) cc_final: 0.7209 (tp30) REVERT: S 62 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7313 (mt0) REVERT: S 76 GLU cc_start: 0.4131 (tp30) cc_final: 0.3775 (tp30) REVERT: S 81 ARG cc_start: 0.6918 (tmm-80) cc_final: 0.6635 (ttp-170) REVERT: S 89 SER cc_start: 0.5394 (p) cc_final: 0.5132 (p) REVERT: S 92 ASP cc_start: 0.6876 (m-30) cc_final: 0.6648 (m-30) REVERT: S 97 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6029 (mm-30) REVERT: S 118 GLN cc_start: 0.5744 (tp-100) cc_final: 0.4870 (pt0) REVERT: T 21 ASP cc_start: 0.8105 (t0) cc_final: 0.7636 (t0) REVERT: T 24 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6717 (mtm-85) REVERT: T 63 GLU cc_start: 0.7220 (tt0) cc_final: 0.6594 (tp30) REVERT: T 78 LYS cc_start: 0.7611 (ttmt) cc_final: 0.7130 (tptt) REVERT: T 91 LYS cc_start: 0.8008 (mttm) cc_final: 0.7283 (mmmt) REVERT: T 112 GLU cc_start: 0.7616 (tt0) cc_final: 0.6774 (tm-30) REVERT: T 127 TRP cc_start: 0.7644 (m-10) cc_final: 0.7320 (m-10) REVERT: U 27 LYS cc_start: 0.7711 (ptpp) cc_final: 0.7212 (mtmt) REVERT: U 98 SER cc_start: 0.8687 (t) cc_final: 0.7904 (p) REVERT: U 116 ASP cc_start: 0.7086 (t0) cc_final: 0.6734 (t0) REVERT: U 118 ASP cc_start: 0.6924 (m-30) cc_final: 0.5935 (t0) REVERT: U 137 GLN cc_start: 0.7732 (mt0) cc_final: 0.7395 (mt0) REVERT: V 19 ARG cc_start: 0.4423 (mpt180) cc_final: 0.3988 (mpp80) REVERT: V 82 MET cc_start: 0.8815 (ttp) cc_final: 0.8535 (ttp) REVERT: W 11 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6866 (pp) REVERT: W 21 ASN cc_start: 0.8231 (t0) cc_final: 0.7213 (t0) REVERT: X 41 MET cc_start: 0.7490 (mtm) cc_final: 0.7054 (mtm) REVERT: X 51 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7617 (pp20) REVERT: X 117 ARG cc_start: 0.6997 (tpp80) cc_final: 0.6411 (mtt-85) REVERT: Y 138 LYS cc_start: 0.8225 (mttt) cc_final: 0.7849 (mtpt) REVERT: Z 8 ARG cc_start: 0.6586 (mtt-85) cc_final: 0.6010 (mmm160) REVERT: Z 17 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7827 (pp) REVERT: Z 22 GLN cc_start: 0.8440 (pt0) cc_final: 0.7963 (pt0) REVERT: Z 47 MET cc_start: 0.7461 (tpp) cc_final: 0.7241 (ttm) REVERT: Z 68 LYS cc_start: 0.7824 (tttt) cc_final: 0.7606 (tttm) REVERT: Z 96 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7027 (pp) REVERT: Z 101 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.5910 (ttmt) REVERT: a 64 ASN cc_start: 0.6488 (m-40) cc_final: 0.6111 (m-40) REVERT: b 38 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7328 (mmtt) REVERT: c 34 ASP cc_start: 0.7503 (m-30) cc_final: 0.7145 (m-30) REVERT: c 45 THR cc_start: 0.8177 (m) cc_final: 0.7855 (t) REVERT: c 75 GLU cc_start: 0.4935 (tp30) cc_final: 0.4552 (tp30) REVERT: e 13 LYS cc_start: 0.8377 (mttm) cc_final: 0.7841 (mtpt) REVERT: e 31 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7983 (mm) REVERT: e 38 MET cc_start: 0.8418 (ttt) cc_final: 0.7746 (ttm) REVERT: f 81 ARG cc_start: 0.6870 (mtp180) cc_final: 0.6381 (mtt-85) REVERT: f 125 LYS cc_start: 0.6317 (mttt) cc_final: 0.6001 (mmtt) REVERT: h 4 GLN cc_start: 0.3858 (tt0) cc_final: 0.2999 (tp40) REVERT: h 5 MET cc_start: 0.5375 (mmp) cc_final: 0.4408 (mmm) REVERT: h 17 TRP cc_start: 0.5977 (OUTLIER) cc_final: 0.2902 (p-90) REVERT: h 149 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.5781 (mp0) REVERT: h 207 CYS cc_start: 0.5831 (OUTLIER) cc_final: 0.5035 (p) REVERT: h 257 LYS cc_start: 0.6385 (ttmp) cc_final: 0.5922 (ttpt) REVERT: h 272 GLN cc_start: 0.4912 (pm20) cc_final: 0.3531 (tp-100) REVERT: h 285 GLN cc_start: 0.7181 (pt0) cc_final: 0.6669 (mt0) REVERT: h 286 CYS cc_start: 0.8109 (t) cc_final: 0.7551 (t) REVERT: h 287 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7439 (p) REVERT: n 2 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7410 (ttt180) outliers start: 212 outliers final: 160 residues processed: 993 average time/residue: 0.8176 time to fit residues: 1351.4176 Evaluate side-chains 1025 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 849 time to evaluate : 4.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 119 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 50 GLN Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain N residue 106 CYS Chi-restraints excluded: chain O residue 13 GLN Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 45 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 36 SER Chi-restraints excluded: chain P residue 54 CYS Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 CYS Chi-restraints excluded: chain P residue 114 SER Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 37 TYR Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain S residue 50 ILE Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 90 VAL Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 34 MET Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain X residue 27 ILE Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 72 CYS Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain Z residue 101 LYS Chi-restraints excluded: chain Z residue 103 SER Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 74 CYS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain c residue 6 ASP Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain d residue 26 GLN Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain e residue 6 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 91 LYS Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 207 CYS Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 287 THR Chi-restraints excluded: chain n residue 2 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 379 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 404 optimal weight: 0.9980 chunk 433 optimal weight: 0.3980 chunk 314 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 500 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN E 174 HIS ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS F 179 ASN F 224 ASN J 7 ASN J 165 GLN K 177 ASN M 108 ASN M 141 ASN ** Q 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Y 97 ASN Z 94 HIS Z 106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 84823 Z= 0.136 Angle : 0.547 11.970 123619 Z= 0.276 Chirality : 0.035 0.458 15363 Planarity : 0.004 0.050 8630 Dihedral : 23.799 179.950 35068 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 3.84 % Allowed : 20.21 % Favored : 75.95 % 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: -0.43 (0.12), residues: 4788 helix: 1.21 (0.13), residues: 1565 sheet: -0.99 (0.17), residues: 900 loop : -1.01 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP h 17 HIS 0.029 0.001 HIS Q 79 PHE 0.022 0.001 PHE C 223 TYR 0.030 0.001 TYR Q 97 ARG 0.009 0.000 ARG E 65 *********************** 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 1060 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 899 time to evaluate : 4.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.7648 (tttt) cc_final: 0.7185 (ttpt) REVERT: B 69 GLU cc_start: 0.7666 (tt0) cc_final: 0.6927 (tp30) REVERT: B 75 SER cc_start: 0.8590 (t) cc_final: 0.8375 (m) REVERT: B 176 TRP cc_start: 0.7663 (t60) cc_final: 0.7439 (t60) REVERT: B 181 GLU cc_start: 0.7058 (tp30) cc_final: 0.6546 (tp30) REVERT: B 192 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5626 (mp0) REVERT: C 42 ARG cc_start: 0.6836 (mmm-85) cc_final: 0.6554 (mmm160) REVERT: C 56 LYS cc_start: 0.7081 (pttt) cc_final: 0.6581 (mmmt) REVERT: C 89 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7310 (mm-30) REVERT: C 103 MET cc_start: 0.8496 (tmm) cc_final: 0.8185 (tmm) REVERT: C 122 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8276 (mt-10) REVERT: C 144 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7404 (tttm) REVERT: C 182 LYS cc_start: 0.7173 (tmtt) cc_final: 0.6875 (ttmt) REVERT: C 230 GLU cc_start: 0.7363 (tt0) cc_final: 0.6947 (tp30) REVERT: D 120 GLN cc_start: 0.8470 (mp10) cc_final: 0.8120 (mp10) REVERT: D 144 SER cc_start: 0.8134 (t) cc_final: 0.7639 (m) REVERT: D 161 SER cc_start: 0.8807 (t) cc_final: 0.8312 (p) REVERT: D 213 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7549 (mt) REVERT: D 215 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6991 (mp) REVERT: E 1 MET cc_start: 0.5236 (ttt) cc_final: 0.4512 (ptp) REVERT: E 31 GLU cc_start: 0.6895 (pm20) cc_final: 0.6545 (pm20) REVERT: E 65 ARG cc_start: 0.4918 (mtp85) cc_final: 0.4534 (ttp-170) REVERT: E 74 GLN cc_start: 0.7874 (tt0) cc_final: 0.7574 (mt0) REVERT: E 83 SER cc_start: 0.6670 (t) cc_final: 0.6232 (m) REVERT: E 84 VAL cc_start: 0.6893 (p) cc_final: 0.6665 (p) REVERT: E 87 TYR cc_start: 0.6318 (m-80) cc_final: 0.5645 (m-80) REVERT: E 89 GLU cc_start: 0.5801 (mt-10) cc_final: 0.5363 (tt0) REVERT: E 90 LYS cc_start: 0.7522 (tttt) cc_final: 0.6467 (tptt) REVERT: E 91 VAL cc_start: 0.5184 (t) cc_final: 0.4982 (p) REVERT: E 107 TYR cc_start: 0.6518 (m-80) cc_final: 0.5661 (m-80) REVERT: E 117 ARG cc_start: 0.7075 (tpt-90) cc_final: 0.6313 (ttm110) REVERT: E 120 TYR cc_start: 0.8189 (m-80) cc_final: 0.6365 (t80) REVERT: E 125 PHE cc_start: 0.7269 (t80) cc_final: 0.6787 (t80) REVERT: E 127 MET cc_start: 0.6835 (tpt) cc_final: 0.6555 (tpt) REVERT: E 146 ARG cc_start: 0.7552 (tpp80) cc_final: 0.5837 (ptm160) REVERT: E 169 ASP cc_start: 0.8451 (t70) cc_final: 0.8119 (t70) REVERT: F 7 LYS cc_start: 0.7873 (mttt) cc_final: 0.7582 (mtmt) REVERT: F 32 SER cc_start: 0.8500 (t) cc_final: 0.8280 (p) REVERT: F 39 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7525 (mtp-110) REVERT: F 79 ASP cc_start: 0.7543 (t0) cc_final: 0.6807 (t70) REVERT: F 87 MET cc_start: 0.7879 (mmt) cc_final: 0.7620 (mmt) REVERT: F 97 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6559 (mm-30) REVERT: F 118 GLU cc_start: 0.6260 (mm-30) cc_final: 0.6041 (tp30) REVERT: F 163 ASP cc_start: 0.7222 (t0) cc_final: 0.6864 (t0) REVERT: F 240 ARG cc_start: 0.6908 (ttp-110) cc_final: 0.5350 (tmm160) REVERT: F 255 ARG cc_start: 0.7293 (ttp80) cc_final: 0.6929 (ptm-80) REVERT: G 37 ASP cc_start: 0.8069 (t70) cc_final: 0.7765 (m-30) REVERT: G 56 TYR cc_start: 0.8166 (m-80) cc_final: 0.7836 (m-80) REVERT: G 65 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7399 (mm-40) REVERT: G 160 GLU cc_start: 0.7308 (tt0) cc_final: 0.6938 (tt0) REVERT: H 12 CYS cc_start: 0.5975 (t) cc_final: 0.5361 (m) REVERT: H 31 ARG cc_start: 0.6124 (ttm110) cc_final: 0.5905 (ttm110) REVERT: H 44 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6923 (tt0) REVERT: H 84 TYR cc_start: 0.7394 (t80) cc_final: 0.7069 (t80) REVERT: H 89 THR cc_start: 0.8703 (m) cc_final: 0.8485 (p) REVERT: H 131 ARG cc_start: 0.5516 (mpt90) cc_final: 0.4437 (ptm-80) REVERT: H 154 ARG cc_start: 0.6293 (mpt-90) cc_final: 0.5831 (mpp80) REVERT: H 200 LYS cc_start: 0.7252 (tttt) cc_final: 0.6634 (mptt) REVERT: H 203 LYS cc_start: 0.7506 (tttt) cc_final: 0.6962 (ptmt) REVERT: H 217 MET cc_start: 0.5927 (tpp) cc_final: 0.5538 (mmp) REVERT: I 57 ARG cc_start: 0.4579 (mmm-85) cc_final: 0.4051 (mmp80) REVERT: I 58 LYS cc_start: 0.7096 (mttt) cc_final: 0.6558 (pttp) REVERT: I 107 LYS cc_start: 0.5605 (mttt) cc_final: 0.5108 (pttt) REVERT: I 163 GLN cc_start: 0.6633 (tt0) cc_final: 0.5943 (tm-30) REVERT: J 77 ARG cc_start: 0.6752 (ttp-170) cc_final: 0.6185 (ttm170) REVERT: J 92 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.6857 (ptm-80) REVERT: J 95 THR cc_start: 0.8276 (m) cc_final: 0.7978 (p) REVERT: J 144 LYS cc_start: 0.6665 (ptpt) cc_final: 0.6092 (mmtt) REVERT: J 157 LYS cc_start: 0.6855 (tppt) cc_final: 0.6304 (mppt) REVERT: J 167 GLN cc_start: 0.6485 (tt0) cc_final: 0.6158 (tp40) REVERT: K 17 ARG cc_start: 0.7811 (ttt90) cc_final: 0.6651 (ttm-80) REVERT: K 18 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7623 (mmt180) REVERT: K 34 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6690 (mp0) REVERT: K 88 ASP cc_start: 0.8213 (m-30) cc_final: 0.7991 (m-30) REVERT: K 101 LYS cc_start: 0.7484 (ptmt) cc_final: 0.7095 (mmmt) REVERT: K 112 THR cc_start: 0.8293 (p) cc_final: 0.8085 (t) REVERT: K 138 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6844 (mtt-85) REVERT: K 165 TYR cc_start: 0.8060 (m-10) cc_final: 0.7806 (m-10) REVERT: L 16 PHE cc_start: 0.7054 (t80) cc_final: 0.6831 (t80) REVERT: L 26 ASP cc_start: 0.8053 (t0) cc_final: 0.7701 (t0) REVERT: M 45 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7852 (mtpt) REVERT: M 97 ARG cc_start: 0.6965 (ptt90) cc_final: 0.6115 (ttt90) REVERT: N 102 LYS cc_start: 0.4576 (ttpt) cc_final: 0.4198 (mmmt) REVERT: O 19 ARG cc_start: 0.7173 (ppt170) cc_final: 0.6750 (mtm180) REVERT: O 27 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6142 (mmtp) REVERT: O 35 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6787 (tp30) REVERT: O 63 VAL cc_start: 0.7801 (t) cc_final: 0.7522 (p) REVERT: O 106 ARG cc_start: 0.7884 (mmt90) cc_final: 0.7136 (ttp-110) REVERT: P 75 MET cc_start: 0.7537 (ttp) cc_final: 0.7177 (tmm) REVERT: P 80 ASP cc_start: 0.8177 (t0) cc_final: 0.7879 (t0) REVERT: P 143 LYS cc_start: 0.8044 (tmmt) cc_final: 0.7558 (tppt) REVERT: Q 34 MET cc_start: 0.7752 (mtt) cc_final: 0.6997 (mtp) REVERT: Q 35 GLN cc_start: 0.7997 (mt0) cc_final: 0.7117 (mp10) REVERT: Q 106 GLU cc_start: 0.6408 (pt0) cc_final: 0.5886 (tm-30) REVERT: Q 108 LYS cc_start: 0.7268 (ptpt) cc_final: 0.6912 (mmtm) REVERT: Q 111 MET cc_start: 0.6942 (mmt) cc_final: 0.5682 (mtt) REVERT: R 102 GLU cc_start: 0.7584 (tt0) cc_final: 0.7383 (tp30) REVERT: S 76 GLU cc_start: 0.4264 (tp30) cc_final: 0.3902 (tp30) REVERT: S 81 ARG cc_start: 0.6946 (tmm-80) cc_final: 0.6578 (ttp-170) REVERT: S 89 SER cc_start: 0.5443 (p) cc_final: 0.5192 (p) REVERT: S 92 ASP cc_start: 0.6893 (m-30) cc_final: 0.6651 (m-30) REVERT: S 97 GLU cc_start: 0.6980 (mt-10) cc_final: 0.5910 (mm-30) REVERT: S 118 GLN cc_start: 0.5509 (tp-100) cc_final: 0.4582 (pt0) REVERT: T 21 ASP cc_start: 0.8146 (t0) cc_final: 0.7716 (t0) REVERT: T 24 ARG cc_start: 0.7221 (mtp85) cc_final: 0.6956 (mtm-85) REVERT: T 78 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7274 (tptt) REVERT: T 91 LYS cc_start: 0.7848 (mttm) cc_final: 0.7115 (mmmt) REVERT: T 112 GLU cc_start: 0.7645 (tt0) cc_final: 0.6654 (tm-30) REVERT: T 127 TRP cc_start: 0.7610 (m-10) cc_final: 0.7295 (m-10) REVERT: U 27 LYS cc_start: 0.7618 (ptpp) cc_final: 0.7143 (mtmt) REVERT: U 98 SER cc_start: 0.8697 (t) cc_final: 0.7954 (p) REVERT: U 116 ASP cc_start: 0.7017 (t0) cc_final: 0.6751 (t0) REVERT: U 118 ASP cc_start: 0.6728 (m-30) cc_final: 0.5710 (t0) REVERT: U 137 GLN cc_start: 0.7670 (mt0) cc_final: 0.7325 (mt0) REVERT: V 19 ARG cc_start: 0.4070 (mpt180) cc_final: 0.3660 (mpp80) REVERT: W 7 GLU cc_start: 0.5501 (pt0) cc_final: 0.4948 (tt0) REVERT: W 11 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6758 (pp) REVERT: W 15 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7527 (mtp180) REVERT: W 21 ASN cc_start: 0.8115 (t0) cc_final: 0.7106 (t0) REVERT: X 41 MET cc_start: 0.7475 (mtm) cc_final: 0.7031 (mtm) REVERT: X 51 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: X 117 ARG cc_start: 0.7051 (tpp80) cc_final: 0.6343 (mtt-85) REVERT: Y 138 LYS cc_start: 0.8252 (mttt) cc_final: 0.7936 (mtpt) REVERT: Y 139 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7141 (tm-30) REVERT: Z 8 ARG cc_start: 0.6571 (mtt-85) cc_final: 0.5992 (mmm160) REVERT: Z 17 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7722 (mt) REVERT: Z 22 GLN cc_start: 0.8344 (pt0) cc_final: 0.7799 (pt0) REVERT: Z 25 ILE cc_start: 0.8338 (mp) cc_final: 0.8109 (mm) REVERT: Z 68 LYS cc_start: 0.7734 (tttt) cc_final: 0.7518 (tttm) REVERT: Z 96 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7001 (pp) REVERT: Z 101 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.5958 (ttmt) REVERT: a 60 LYS cc_start: 0.7329 (tppt) cc_final: 0.7046 (ttpt) REVERT: a 64 ASN cc_start: 0.6398 (m-40) cc_final: 0.6044 (m-40) REVERT: a 111 ARG cc_start: 0.6092 (ptt180) cc_final: 0.5888 (ptt180) REVERT: b 25 ASN cc_start: 0.8085 (t0) cc_final: 0.7836 (t0) REVERT: b 38 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7272 (mmtt) REVERT: b 85 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7013 (mtt-85) REVERT: b 86 ASN cc_start: 0.8640 (p0) cc_final: 0.8431 (p0) REVERT: c 34 ASP cc_start: 0.7470 (m-30) cc_final: 0.7115 (m-30) REVERT: c 45 THR cc_start: 0.8178 (m) cc_final: 0.7842 (t) REVERT: c 75 GLU cc_start: 0.4734 (tp30) cc_final: 0.4462 (tp30) REVERT: d 35 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.5995 (mmm) REVERT: e 13 LYS cc_start: 0.8359 (mttm) cc_final: 0.7820 (mtpt) REVERT: e 38 MET cc_start: 0.8190 (ttt) cc_final: 0.7625 (ttm) REVERT: f 125 LYS cc_start: 0.6522 (mttt) cc_final: 0.6156 (mmtt) REVERT: g 140 TYR cc_start: 0.3555 (OUTLIER) cc_final: 0.2703 (t80) REVERT: h 4 GLN cc_start: 0.3850 (tt0) cc_final: 0.2978 (tp-100) REVERT: h 5 MET cc_start: 0.5277 (mmp) cc_final: 0.4607 (mmm) REVERT: h 17 TRP cc_start: 0.5842 (OUTLIER) cc_final: 0.2640 (p-90) REVERT: h 149 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.5905 (mp0) REVERT: h 207 CYS cc_start: 0.5381 (OUTLIER) cc_final: 0.4630 (p) REVERT: h 257 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5927 (ttpt) REVERT: h 272 GLN cc_start: 0.4818 (pm20) cc_final: 0.3477 (tp-100) REVERT: h 285 GLN cc_start: 0.6959 (pt0) cc_final: 0.6576 (mt0) REVERT: h 286 CYS cc_start: 0.7581 (t) cc_final: 0.7112 (t) REVERT: h 287 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7308 (p) outliers start: 161 outliers final: 96 residues processed: 996 average time/residue: 0.8170 time to fit residues: 1356.4597 Evaluate side-chains 965 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 854 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 106 CYS Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 83 ASP Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 CYS Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 83 ASN Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain Z residue 101 LYS Chi-restraints excluded: chain Z residue 103 SER Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain e residue 49 ASP Chi-restraints excluded: chain f residue 91 LYS Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain g residue 140 TYR Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 32 LEU Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 207 CYS Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 287 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 0.0030 chunk 609 optimal weight: 2.9990 chunk 556 optimal weight: 5.9990 chunk 592 optimal weight: 2.9990 chunk 356 optimal weight: 0.0570 chunk 258 optimal weight: 20.0000 chunk 465 optimal weight: 0.2980 chunk 181 optimal weight: 0.9990 chunk 535 optimal weight: 2.9990 chunk 560 optimal weight: 1.9990 chunk 590 optimal weight: 3.9990 overall best weight: 0.6712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN E 174 HIS E 179 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 224 ASN H 59 GLN K 177 ASN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Y 97 ASN Z 106 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 84823 Z= 0.133 Angle : 0.535 10.581 123619 Z= 0.269 Chirality : 0.034 0.434 15363 Planarity : 0.004 0.050 8630 Dihedral : 23.709 179.438 35066 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 3.22 % Allowed : 21.04 % Favored : 75.74 % 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: -0.26 (0.12), residues: 4788 helix: 1.32 (0.13), residues: 1564 sheet: -0.78 (0.17), residues: 882 loop : -0.93 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP h 17 HIS 0.016 0.001 HIS Q 79 PHE 0.023 0.001 PHE C 223 TYR 0.018 0.001 TYR L 12 ARG 0.008 0.000 ARG S 67 *********************** 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 1005 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 870 time to evaluate : 4.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.7664 (tttt) cc_final: 0.7092 (ttpt) REVERT: B 69 GLU cc_start: 0.7748 (tt0) cc_final: 0.7006 (tp30) REVERT: B 181 GLU cc_start: 0.6653 (tp30) cc_final: 0.6115 (tp30) REVERT: B 192 GLU cc_start: 0.6208 (mm-30) cc_final: 0.5617 (mp0) REVERT: C 42 ARG cc_start: 0.6790 (mmm-85) cc_final: 0.6479 (mmm160) REVERT: C 56 LYS cc_start: 0.7071 (pttt) cc_final: 0.6563 (mmmt) REVERT: C 103 MET cc_start: 0.8563 (tmm) cc_final: 0.8250 (tmm) REVERT: C 122 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8287 (mt-10) REVERT: C 144 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7367 (tttm) REVERT: C 182 LYS cc_start: 0.7169 (tmtt) cc_final: 0.6862 (ttmt) REVERT: C 230 GLU cc_start: 0.7378 (tt0) cc_final: 0.6951 (tp30) REVERT: D 120 GLN cc_start: 0.8503 (mp10) cc_final: 0.8173 (mp10) REVERT: D 121 ARG cc_start: 0.7385 (tpm-80) cc_final: 0.7071 (ttm-80) REVERT: D 144 SER cc_start: 0.8115 (t) cc_final: 0.7620 (m) REVERT: D 161 SER cc_start: 0.8818 (t) cc_final: 0.8307 (p) REVERT: D 213 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7477 (mt) REVERT: D 215 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6900 (mp) REVERT: E 1 MET cc_start: 0.5232 (ttt) cc_final: 0.4508 (ptp) REVERT: E 31 GLU cc_start: 0.6845 (pm20) cc_final: 0.6505 (pm20) REVERT: E 65 ARG cc_start: 0.5045 (mtp85) cc_final: 0.4521 (ttp-170) REVERT: E 74 GLN cc_start: 0.7882 (tt0) cc_final: 0.7572 (mt0) REVERT: E 83 SER cc_start: 0.6657 (t) cc_final: 0.6218 (m) REVERT: E 84 VAL cc_start: 0.6921 (p) cc_final: 0.6720 (p) REVERT: E 87 TYR cc_start: 0.6448 (m-80) cc_final: 0.5853 (m-80) REVERT: E 89 GLU cc_start: 0.5758 (mt-10) cc_final: 0.5318 (tt0) REVERT: E 90 LYS cc_start: 0.7448 (tttt) cc_final: 0.6392 (tptt) REVERT: E 107 TYR cc_start: 0.6433 (m-80) cc_final: 0.5569 (m-80) REVERT: E 117 ARG cc_start: 0.7082 (tpt-90) cc_final: 0.6295 (ttm110) REVERT: E 120 TYR cc_start: 0.8117 (m-80) cc_final: 0.6222 (t80) REVERT: E 125 PHE cc_start: 0.7236 (t80) cc_final: 0.6776 (t80) REVERT: E 127 MET cc_start: 0.6993 (tpt) cc_final: 0.6730 (tpt) REVERT: E 146 ARG cc_start: 0.7478 (tpp80) cc_final: 0.5824 (ptm160) REVERT: E 169 ASP cc_start: 0.8435 (t70) cc_final: 0.8083 (t70) REVERT: F 7 LYS cc_start: 0.7898 (mttt) cc_final: 0.7612 (mtmt) REVERT: F 32 SER cc_start: 0.8567 (t) cc_final: 0.8324 (p) REVERT: F 39 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7514 (mtp-110) REVERT: F 79 ASP cc_start: 0.7447 (t0) cc_final: 0.6716 (t70) REVERT: F 97 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6536 (mm-30) REVERT: F 118 GLU cc_start: 0.6549 (mm-30) cc_final: 0.6312 (tp30) REVERT: F 163 ASP cc_start: 0.7152 (t0) cc_final: 0.6770 (t0) REVERT: F 240 ARG cc_start: 0.6919 (ttp-110) cc_final: 0.5350 (tmm160) REVERT: F 255 ARG cc_start: 0.7257 (ttp80) cc_final: 0.6923 (ptm-80) REVERT: G 37 ASP cc_start: 0.8074 (t70) cc_final: 0.7765 (m-30) REVERT: G 56 TYR cc_start: 0.8168 (m-80) cc_final: 0.7829 (m-80) REVERT: G 65 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7169 (mm-40) REVERT: G 160 GLU cc_start: 0.7297 (tt0) cc_final: 0.6897 (mt-10) REVERT: G 166 ILE cc_start: 0.8316 (mt) cc_final: 0.7993 (tt) REVERT: H 12 CYS cc_start: 0.6011 (t) cc_final: 0.5390 (m) REVERT: H 31 ARG cc_start: 0.6221 (ttm110) cc_final: 0.6016 (ttm110) REVERT: H 44 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6959 (tt0) REVERT: H 84 TYR cc_start: 0.7417 (t80) cc_final: 0.7190 (t80) REVERT: H 131 ARG cc_start: 0.5619 (mpt90) cc_final: 0.4468 (ptm-80) REVERT: H 154 ARG cc_start: 0.6292 (mpt-90) cc_final: 0.5839 (mpp80) REVERT: H 200 LYS cc_start: 0.7251 (tttt) cc_final: 0.6633 (mptt) REVERT: H 203 LYS cc_start: 0.7541 (tttt) cc_final: 0.7013 (ptmt) REVERT: H 217 MET cc_start: 0.5963 (tpp) cc_final: 0.5583 (mmp) REVERT: I 57 ARG cc_start: 0.4518 (mmm-85) cc_final: 0.4014 (mmp80) REVERT: I 58 LYS cc_start: 0.7111 (mttt) cc_final: 0.6566 (pttp) REVERT: I 107 LYS cc_start: 0.5631 (mttt) cc_final: 0.5147 (pttt) REVERT: I 163 GLN cc_start: 0.6494 (tt0) cc_final: 0.5827 (tm-30) REVERT: J 3 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7348 (tp) REVERT: J 37 LYS cc_start: 0.7665 (mmmm) cc_final: 0.7022 (mmtm) REVERT: J 77 ARG cc_start: 0.6765 (ttp-170) cc_final: 0.6199 (ttm170) REVERT: J 92 ARG cc_start: 0.7762 (ttp-170) cc_final: 0.6992 (ttp80) REVERT: J 95 THR cc_start: 0.8305 (m) cc_final: 0.8018 (p) REVERT: J 144 LYS cc_start: 0.6650 (ptpt) cc_final: 0.6071 (mmtt) REVERT: J 157 LYS cc_start: 0.6867 (tppt) cc_final: 0.6337 (mppt) REVERT: J 167 GLN cc_start: 0.6402 (tt0) cc_final: 0.6070 (tp40) REVERT: K 17 ARG cc_start: 0.7817 (ttt90) cc_final: 0.6702 (ttm-80) REVERT: K 18 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7617 (mmt180) REVERT: K 34 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6687 (mp0) REVERT: K 88 ASP cc_start: 0.8214 (m-30) cc_final: 0.7990 (m-30) REVERT: K 101 LYS cc_start: 0.7486 (ptmt) cc_final: 0.7092 (mmmt) REVERT: K 112 THR cc_start: 0.8271 (p) cc_final: 0.8066 (t) REVERT: K 138 ARG cc_start: 0.7155 (mtt180) cc_final: 0.6844 (mtt-85) REVERT: L 2 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5920 (tt) REVERT: L 16 PHE cc_start: 0.7040 (t80) cc_final: 0.6822 (t80) REVERT: L 26 ASP cc_start: 0.8121 (t0) cc_final: 0.7697 (t0) REVERT: M 45 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7838 (mtpt) REVERT: M 97 ARG cc_start: 0.6975 (ptt90) cc_final: 0.6194 (ttt90) REVERT: M 108 ASN cc_start: 0.6763 (p0) cc_final: 0.6528 (p0) REVERT: N 102 LYS cc_start: 0.4582 (ttpt) cc_final: 0.4286 (mmmt) REVERT: O 13 GLN cc_start: 0.7993 (pt0) cc_final: 0.7537 (pt0) REVERT: O 19 ARG cc_start: 0.7149 (ppt170) cc_final: 0.6740 (mtm180) REVERT: O 27 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6092 (mmtp) REVERT: O 106 ARG cc_start: 0.7887 (mmt90) cc_final: 0.7138 (ttp-110) REVERT: P 75 MET cc_start: 0.7456 (ttp) cc_final: 0.7091 (tmm) REVERT: P 80 ASP cc_start: 0.8177 (t0) cc_final: 0.7871 (t0) REVERT: P 143 LYS cc_start: 0.8068 (tmmt) cc_final: 0.7594 (tppt) REVERT: Q 34 MET cc_start: 0.7640 (mtt) cc_final: 0.6734 (mtp) REVERT: Q 35 GLN cc_start: 0.7963 (mt0) cc_final: 0.7059 (mp10) REVERT: Q 64 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7001 (pttt) REVERT: Q 92 SER cc_start: 0.8442 (m) cc_final: 0.7767 (t) REVERT: Q 106 GLU cc_start: 0.6455 (pt0) cc_final: 0.5989 (tm-30) REVERT: Q 108 LYS cc_start: 0.7214 (ptpt) cc_final: 0.6922 (mmtm) REVERT: Q 111 MET cc_start: 0.6907 (mmt) cc_final: 0.5951 (mtt) REVERT: R 129 SER cc_start: 0.8389 (p) cc_final: 0.8058 (m) REVERT: S 76 GLU cc_start: 0.4152 (tp30) cc_final: 0.3812 (tp30) REVERT: S 81 ARG cc_start: 0.6944 (tmm-80) cc_final: 0.6578 (ttp-170) REVERT: S 87 GLU cc_start: 0.7752 (tt0) cc_final: 0.7275 (mm-30) REVERT: S 89 SER cc_start: 0.5294 (p) cc_final: 0.5029 (p) REVERT: S 92 ASP cc_start: 0.6914 (m-30) cc_final: 0.6667 (m-30) REVERT: S 97 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6531 (mm-30) REVERT: S 118 GLN cc_start: 0.5395 (tp-100) cc_final: 0.4917 (tp40) REVERT: T 21 ASP cc_start: 0.7954 (t0) cc_final: 0.7404 (t0) REVERT: T 24 ARG cc_start: 0.7256 (mtp85) cc_final: 0.6998 (mtm-85) REVERT: T 78 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7255 (tptt) REVERT: T 91 LYS cc_start: 0.7713 (mttm) cc_final: 0.7069 (mmmt) REVERT: T 112 GLU cc_start: 0.7586 (tt0) cc_final: 0.6459 (tm-30) REVERT: T 127 TRP cc_start: 0.7622 (m-10) cc_final: 0.7305 (m-10) REVERT: U 27 LYS cc_start: 0.7635 (ptpp) cc_final: 0.7180 (mtmt) REVERT: U 98 SER cc_start: 0.8694 (t) cc_final: 0.7887 (p) REVERT: U 116 ASP cc_start: 0.7037 (t0) cc_final: 0.6754 (t0) REVERT: U 118 ASP cc_start: 0.6746 (m-30) cc_final: 0.5734 (t0) REVERT: V 19 ARG cc_start: 0.3839 (mpt180) cc_final: 0.3502 (mpp80) REVERT: W 7 GLU cc_start: 0.5367 (pt0) cc_final: 0.4914 (tt0) REVERT: W 11 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6802 (pp) REVERT: W 15 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7520 (mtp180) REVERT: W 21 ASN cc_start: 0.8195 (t0) cc_final: 0.7192 (t0) REVERT: X 41 MET cc_start: 0.7488 (mtm) cc_final: 0.7069 (mtm) REVERT: X 51 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: X 117 ARG cc_start: 0.7061 (tpp80) cc_final: 0.6344 (mtt-85) REVERT: Y 108 LYS cc_start: 0.7506 (mttt) cc_final: 0.7282 (mptt) REVERT: Y 138 LYS cc_start: 0.8212 (mttt) cc_final: 0.7298 (mtmm) REVERT: Y 139 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7147 (tm-30) REVERT: Z 8 ARG cc_start: 0.6672 (mtt-85) cc_final: 0.6150 (mmm160) REVERT: Z 17 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7725 (mt) REVERT: Z 22 GLN cc_start: 0.8454 (pt0) cc_final: 0.8101 (pt0) REVERT: Z 25 ILE cc_start: 0.8265 (mp) cc_final: 0.8051 (mm) REVERT: Z 68 LYS cc_start: 0.7551 (tttt) cc_final: 0.7274 (tttm) REVERT: Z 96 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6975 (pp) REVERT: Z 101 LYS cc_start: 0.6341 (OUTLIER) cc_final: 0.5872 (ttmt) REVERT: a 60 LYS cc_start: 0.7424 (tppt) cc_final: 0.7141 (ttpt) REVERT: a 64 ASN cc_start: 0.6447 (m-40) cc_final: 0.6072 (m-40) REVERT: a 102 LYS cc_start: 0.7828 (ttmm) cc_final: 0.7527 (tptm) REVERT: b 38 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7285 (mmtt) REVERT: b 42 ARG cc_start: 0.7392 (mtm110) cc_final: 0.7049 (mtm110) REVERT: b 85 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7006 (mtt-85) REVERT: c 34 ASP cc_start: 0.7473 (m-30) cc_final: 0.7123 (m-30) REVERT: c 45 THR cc_start: 0.8184 (m) cc_final: 0.7870 (t) REVERT: c 75 GLU cc_start: 0.4734 (tp30) cc_final: 0.4469 (tp30) REVERT: d 35 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.5968 (mmm) REVERT: e 13 LYS cc_start: 0.8393 (mttm) cc_final: 0.7858 (mtpt) REVERT: e 31 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7942 (mm) REVERT: e 38 MET cc_start: 0.8276 (ttt) cc_final: 0.7452 (ttm) REVERT: f 91 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7594 (tttt) REVERT: f 125 LYS cc_start: 0.6515 (mttt) cc_final: 0.6153 (mmtt) REVERT: g 140 TYR cc_start: 0.3447 (OUTLIER) cc_final: 0.2767 (t80) REVERT: h 4 GLN cc_start: 0.3880 (tt0) cc_final: 0.3135 (tp-100) REVERT: h 5 MET cc_start: 0.5406 (mmp) cc_final: 0.4544 (mmm) REVERT: h 17 TRP cc_start: 0.5699 (OUTLIER) cc_final: 0.2485 (p-90) REVERT: h 149 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.5875 (mp0) REVERT: h 203 ASP cc_start: 0.7382 (m-30) cc_final: 0.7011 (p0) REVERT: h 207 CYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4554 (p) REVERT: h 257 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5892 (ttpt) REVERT: h 272 GLN cc_start: 0.4660 (pm20) cc_final: 0.3339 (tp-100) REVERT: h 285 GLN cc_start: 0.6972 (pt0) cc_final: 0.6597 (mt0) REVERT: h 286 CYS cc_start: 0.7745 (t) cc_final: 0.7236 (t) REVERT: h 287 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7322 (p) outliers start: 135 outliers final: 98 residues processed: 950 average time/residue: 0.8161 time to fit residues: 1282.9272 Evaluate side-chains 967 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 850 time to evaluate : 4.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 106 CYS Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 CYS Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 83 ASN Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain Z residue 101 LYS Chi-restraints excluded: chain Z residue 103 SER Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 79 ILE Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 91 LYS Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain g residue 140 TYR Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 165 ILE Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 207 CYS Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 0.2980 chunk 626 optimal weight: 0.9990 chunk 382 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 435 optimal weight: 1.9990 chunk 657 optimal weight: 0.0770 chunk 605 optimal weight: 5.9990 chunk 523 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 404 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 224 ASN J 165 GLN K 177 ASN ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN Z 106 GLN d 29 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 84823 Z= 0.129 Angle : 0.531 17.555 123619 Z= 0.265 Chirality : 0.034 0.426 15363 Planarity : 0.004 0.051 8630 Dihedral : 23.653 179.692 35066 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 2.84 % Allowed : 21.59 % Favored : 75.57 % 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: -0.18 (0.12), residues: 4788 helix: 1.35 (0.13), residues: 1563 sheet: -0.66 (0.17), residues: 877 loop : -0.88 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP h 17 HIS 0.014 0.001 HIS Q 79 PHE 0.021 0.001 PHE C 223 TYR 0.020 0.001 TYR h 194 ARG 0.008 0.000 ARG S 67 ********************** 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 998 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 879 time to evaluate : 4.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.7661 (tttt) cc_final: 0.7161 (ttpt) REVERT: B 69 GLU cc_start: 0.7630 (tt0) cc_final: 0.6838 (tp30) REVERT: B 181 GLU cc_start: 0.6870 (tp30) cc_final: 0.6341 (tp30) REVERT: B 192 GLU cc_start: 0.6201 (mm-30) cc_final: 0.5608 (mp0) REVERT: C 42 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.6454 (mmm160) REVERT: C 56 LYS cc_start: 0.7062 (pttt) cc_final: 0.6558 (mmmt) REVERT: C 89 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7280 (mm-30) REVERT: C 103 MET cc_start: 0.8546 (tmm) cc_final: 0.8225 (tmm) REVERT: C 144 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7340 (tttm) REVERT: C 182 LYS cc_start: 0.7165 (tmtt) cc_final: 0.6844 (ttmt) REVERT: C 230 GLU cc_start: 0.7400 (tt0) cc_final: 0.6947 (tp30) REVERT: D 77 SER cc_start: 0.6902 (m) cc_final: 0.6601 (p) REVERT: D 120 GLN cc_start: 0.8526 (mp10) cc_final: 0.8201 (mp10) REVERT: D 121 ARG cc_start: 0.7353 (tpm-80) cc_final: 0.7034 (ttm-80) REVERT: D 144 SER cc_start: 0.8115 (t) cc_final: 0.7609 (m) REVERT: D 161 SER cc_start: 0.8801 (t) cc_final: 0.8275 (p) REVERT: D 213 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7485 (mt) REVERT: D 215 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6937 (mp) REVERT: E 31 GLU cc_start: 0.6797 (pm20) cc_final: 0.6458 (pm20) REVERT: E 32 ASP cc_start: 0.5947 (m-30) cc_final: 0.5728 (m-30) REVERT: E 74 GLN cc_start: 0.7884 (tt0) cc_final: 0.7570 (mt0) REVERT: E 84 VAL cc_start: 0.7145 (p) cc_final: 0.6882 (p) REVERT: E 87 TYR cc_start: 0.6076 (m-80) cc_final: 0.5668 (m-80) REVERT: E 89 GLU cc_start: 0.6331 (mt-10) cc_final: 0.5989 (tt0) REVERT: E 90 LYS cc_start: 0.7599 (tttt) cc_final: 0.6444 (tptt) REVERT: E 107 TYR cc_start: 0.6402 (m-80) cc_final: 0.5542 (m-80) REVERT: E 117 ARG cc_start: 0.7086 (tpt-90) cc_final: 0.6311 (ttm110) REVERT: E 120 TYR cc_start: 0.8066 (m-80) cc_final: 0.6013 (t80) REVERT: E 125 PHE cc_start: 0.7211 (t80) cc_final: 0.6862 (t80) REVERT: E 146 ARG cc_start: 0.7393 (tpp80) cc_final: 0.5665 (ptm160) REVERT: E 169 ASP cc_start: 0.8418 (t70) cc_final: 0.8091 (t70) REVERT: F 7 LYS cc_start: 0.7920 (mttt) cc_final: 0.7629 (mtmt) REVERT: F 32 SER cc_start: 0.8560 (t) cc_final: 0.8323 (p) REVERT: F 39 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7516 (mtp-110) REVERT: F 79 ASP cc_start: 0.7525 (t0) cc_final: 0.7219 (t0) REVERT: F 87 MET cc_start: 0.7901 (mmt) cc_final: 0.7679 (mmt) REVERT: F 97 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6517 (mm-30) REVERT: F 118 GLU cc_start: 0.6526 (mm-30) cc_final: 0.6309 (tp30) REVERT: F 163 ASP cc_start: 0.7148 (t0) cc_final: 0.6760 (t0) REVERT: F 240 ARG cc_start: 0.6924 (ttp-110) cc_final: 0.5350 (tmm160) REVERT: F 255 ARG cc_start: 0.7251 (ttp80) cc_final: 0.6919 (ptm-80) REVERT: G 37 ASP cc_start: 0.8083 (t70) cc_final: 0.7766 (m-30) REVERT: G 56 TYR cc_start: 0.8169 (m-80) cc_final: 0.7833 (m-80) REVERT: G 160 GLU cc_start: 0.7404 (tt0) cc_final: 0.7023 (mt-10) REVERT: G 166 ILE cc_start: 0.8308 (mt) cc_final: 0.8004 (tt) REVERT: H 12 CYS cc_start: 0.5983 (t) cc_final: 0.5376 (m) REVERT: H 31 ARG cc_start: 0.6245 (ttm110) cc_final: 0.6044 (ttm110) REVERT: H 35 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6260 (mt-10) REVERT: H 44 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6958 (tt0) REVERT: H 59 GLN cc_start: 0.7058 (mp10) cc_final: 0.6531 (mp10) REVERT: H 84 TYR cc_start: 0.7429 (t80) cc_final: 0.7209 (t80) REVERT: H 131 ARG cc_start: 0.5470 (mpt90) cc_final: 0.4423 (ptm160) REVERT: H 154 ARG cc_start: 0.6258 (mpt-90) cc_final: 0.5795 (mpp80) REVERT: H 200 LYS cc_start: 0.7251 (tttt) cc_final: 0.6633 (mptt) REVERT: H 203 LYS cc_start: 0.7362 (tttt) cc_final: 0.6908 (ptmt) REVERT: H 217 MET cc_start: 0.5858 (tpp) cc_final: 0.5490 (mmp) REVERT: I 57 ARG cc_start: 0.4545 (mmm-85) cc_final: 0.3895 (mmp80) REVERT: I 58 LYS cc_start: 0.7104 (mttt) cc_final: 0.6534 (pttp) REVERT: I 107 LYS cc_start: 0.5619 (mttt) cc_final: 0.5139 (pttt) REVERT: I 163 GLN cc_start: 0.6477 (tt0) cc_final: 0.5815 (tm-30) REVERT: J 3 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7434 (tp) REVERT: J 37 LYS cc_start: 0.7694 (mmmm) cc_final: 0.7063 (mmtm) REVERT: J 77 ARG cc_start: 0.6851 (ttp-170) cc_final: 0.6219 (ttm170) REVERT: J 92 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.6996 (ttp80) REVERT: J 95 THR cc_start: 0.8294 (m) cc_final: 0.8008 (p) REVERT: J 144 LYS cc_start: 0.6624 (ptpt) cc_final: 0.6048 (mmtt) REVERT: J 157 LYS cc_start: 0.6907 (tppt) cc_final: 0.6332 (mppt) REVERT: J 167 GLN cc_start: 0.6453 (tt0) cc_final: 0.6091 (tp40) REVERT: K 17 ARG cc_start: 0.7798 (ttt90) cc_final: 0.6690 (ttm-80) REVERT: K 18 ARG cc_start: 0.8004 (mtt90) cc_final: 0.7608 (mmt180) REVERT: K 34 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6672 (mp0) REVERT: K 88 ASP cc_start: 0.8218 (m-30) cc_final: 0.7992 (m-30) REVERT: K 101 LYS cc_start: 0.7549 (ptmt) cc_final: 0.7048 (mmmt) REVERT: K 112 THR cc_start: 0.8319 (p) cc_final: 0.8105 (t) REVERT: L 3 MET cc_start: 0.6140 (mtt) cc_final: 0.5743 (ptp) REVERT: L 16 PHE cc_start: 0.6753 (t80) cc_final: 0.6521 (t80) REVERT: L 26 ASP cc_start: 0.8084 (t0) cc_final: 0.7707 (t0) REVERT: M 45 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7895 (mtpt) REVERT: M 97 ARG cc_start: 0.6946 (ptt90) cc_final: 0.6185 (ttt90) REVERT: M 108 ASN cc_start: 0.6626 (p0) cc_final: 0.6363 (p0) REVERT: N 102 LYS cc_start: 0.4624 (ttpt) cc_final: 0.4185 (tttp) REVERT: O 13 GLN cc_start: 0.7956 (pt0) cc_final: 0.7560 (pt0) REVERT: O 19 ARG cc_start: 0.7146 (ppt170) cc_final: 0.6720 (mtm180) REVERT: O 27 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.5959 (mmtp) REVERT: O 63 VAL cc_start: 0.7781 (t) cc_final: 0.7492 (p) REVERT: O 106 ARG cc_start: 0.7893 (mmt90) cc_final: 0.7138 (ttp-110) REVERT: P 75 MET cc_start: 0.7485 (ttp) cc_final: 0.7115 (tmm) REVERT: P 80 ASP cc_start: 0.8191 (t0) cc_final: 0.7890 (t0) REVERT: P 143 LYS cc_start: 0.8066 (tmmt) cc_final: 0.7589 (tppt) REVERT: Q 34 MET cc_start: 0.7636 (mtt) cc_final: 0.6654 (mtp) REVERT: Q 35 GLN cc_start: 0.8080 (mt0) cc_final: 0.7198 (mp10) REVERT: Q 64 LYS cc_start: 0.7976 (mmtt) cc_final: 0.6952 (ptpt) REVERT: Q 92 SER cc_start: 0.8502 (m) cc_final: 0.7810 (t) REVERT: Q 106 GLU cc_start: 0.6432 (pt0) cc_final: 0.5999 (tm-30) REVERT: Q 108 LYS cc_start: 0.7162 (ptpt) cc_final: 0.6909 (mmtm) REVERT: Q 111 MET cc_start: 0.6881 (mmt) cc_final: 0.5717 (mtt) REVERT: R 102 GLU cc_start: 0.7862 (tp30) cc_final: 0.7515 (tp30) REVERT: R 129 SER cc_start: 0.8429 (p) cc_final: 0.8120 (m) REVERT: S 76 GLU cc_start: 0.4146 (tp30) cc_final: 0.3812 (tp30) REVERT: S 81 ARG cc_start: 0.6946 (tmm-80) cc_final: 0.6572 (ttp-170) REVERT: S 87 GLU cc_start: 0.7747 (tt0) cc_final: 0.7273 (mm-30) REVERT: S 89 SER cc_start: 0.5288 (p) cc_final: 0.5003 (p) REVERT: S 92 ASP cc_start: 0.6800 (m-30) cc_final: 0.6576 (m-30) REVERT: S 97 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6530 (mm-30) REVERT: S 107 LYS cc_start: 0.6715 (ttpt) cc_final: 0.6402 (pttt) REVERT: S 118 GLN cc_start: 0.5356 (tp-100) cc_final: 0.4946 (tp40) REVERT: T 21 ASP cc_start: 0.7998 (t0) cc_final: 0.7447 (t0) REVERT: T 24 ARG cc_start: 0.7308 (mtp85) cc_final: 0.7066 (mtm-85) REVERT: T 78 LYS cc_start: 0.7748 (ttmt) cc_final: 0.7333 (tptt) REVERT: T 91 LYS cc_start: 0.7590 (mttm) cc_final: 0.7010 (mmmt) REVERT: T 112 GLU cc_start: 0.7441 (tt0) cc_final: 0.6754 (tp30) REVERT: T 127 TRP cc_start: 0.7635 (m-10) cc_final: 0.7303 (m-10) REVERT: U 27 LYS cc_start: 0.7625 (ptpp) cc_final: 0.7185 (mtmt) REVERT: U 98 SER cc_start: 0.8685 (t) cc_final: 0.7882 (p) REVERT: U 116 ASP cc_start: 0.7007 (t0) cc_final: 0.6747 (t0) REVERT: V 19 ARG cc_start: 0.3877 (mpt180) cc_final: 0.3500 (mpp80) REVERT: W 7 GLU cc_start: 0.5362 (pt0) cc_final: 0.4913 (tt0) REVERT: W 11 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6771 (pp) REVERT: W 21 ASN cc_start: 0.8193 (t0) cc_final: 0.7200 (t0) REVERT: X 51 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7405 (pp20) REVERT: X 117 ARG cc_start: 0.7073 (tpp80) cc_final: 0.6348 (mtt-85) REVERT: Y 138 LYS cc_start: 0.8179 (mttt) cc_final: 0.7242 (mtmm) REVERT: Y 139 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7150 (tm-30) REVERT: Z 8 ARG cc_start: 0.6657 (mtt-85) cc_final: 0.6122 (mmm160) REVERT: Z 17 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7738 (mt) REVERT: Z 22 GLN cc_start: 0.8476 (pt0) cc_final: 0.8126 (pt0) REVERT: Z 68 LYS cc_start: 0.7566 (tttt) cc_final: 0.7291 (tttm) REVERT: Z 96 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6970 (pp) REVERT: Z 101 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5913 (ttmt) REVERT: a 60 LYS cc_start: 0.7471 (tppt) cc_final: 0.7205 (ttpt) REVERT: a 64 ASN cc_start: 0.6426 (m-40) cc_final: 0.6045 (m-40) REVERT: a 102 LYS cc_start: 0.7820 (ttmm) cc_final: 0.7585 (tptm) REVERT: b 25 ASN cc_start: 0.8039 (t0) cc_final: 0.7806 (t0) REVERT: b 38 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7321 (mmtt) REVERT: b 42 ARG cc_start: 0.7420 (mtm110) cc_final: 0.7063 (mtm110) REVERT: b 85 ARG cc_start: 0.7667 (ttm110) cc_final: 0.7034 (mtt-85) REVERT: c 34 ASP cc_start: 0.7445 (m-30) cc_final: 0.7155 (m-30) REVERT: c 45 THR cc_start: 0.8178 (m) cc_final: 0.7833 (t) REVERT: d 35 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6168 (mmt) REVERT: e 13 LYS cc_start: 0.8374 (mttm) cc_final: 0.7841 (mtpt) REVERT: e 38 MET cc_start: 0.8231 (ttt) cc_final: 0.7371 (ttm) REVERT: f 91 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7596 (tttt) REVERT: f 125 LYS cc_start: 0.6507 (mttt) cc_final: 0.6152 (mmtt) REVERT: h 4 GLN cc_start: 0.3879 (tt0) cc_final: 0.3131 (tp-100) REVERT: h 5 MET cc_start: 0.5402 (mmp) cc_final: 0.4515 (mmm) REVERT: h 17 TRP cc_start: 0.5743 (OUTLIER) cc_final: 0.2345 (p-90) REVERT: h 149 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.5868 (mp0) REVERT: h 203 ASP cc_start: 0.7352 (m-30) cc_final: 0.6993 (p0) REVERT: h 207 CYS cc_start: 0.5313 (OUTLIER) cc_final: 0.4645 (p) REVERT: h 257 LYS cc_start: 0.6350 (OUTLIER) cc_final: 0.5847 (ttpt) REVERT: h 272 GLN cc_start: 0.4648 (pm20) cc_final: 0.3336 (tp-100) REVERT: h 285 GLN cc_start: 0.6981 (pt0) cc_final: 0.6615 (mt0) REVERT: h 286 CYS cc_start: 0.7661 (t) cc_final: 0.7159 (t) REVERT: h 287 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7276 (p) outliers start: 119 outliers final: 90 residues processed: 945 average time/residue: 0.8957 time to fit residues: 1424.8530 Evaluate side-chains 950 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 844 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 70 HIS Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 6 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain N residue 106 CYS Chi-restraints excluded: chain O residue 27 LYS Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 134 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 CYS Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 107 ILE Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain S residue 83 ASN Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 6 VAL Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain V residue 65 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 47 ASN Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain X residue 51 GLU Chi-restraints excluded: chain X residue 80 ASP Chi-restraints excluded: chain X residue 103 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain Y residue 115 ILE Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 17 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain Z residue 101 LYS Chi-restraints excluded: chain Z residue 103 SER Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 70 LYS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 35 MET Chi-restraints excluded: chain f residue 91 LYS Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain h residue 17 TRP Chi-restraints excluded: chain h residue 111 VAL Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 207 CYS Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 287 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 2.9990 chunk 557 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 482 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 524 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 538 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN C 40 ASN E 174 HIS ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN K 177 ASN ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS X 24 GLN Z 106 GLN ** f 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 ASN h 191 HIS h 215 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122391 restraints weight = 119666.585| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.07 r_work: 0.3221 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 84823 Z= 0.376 Angle : 0.717 16.196 123619 Z= 0.359 Chirality : 0.043 0.413 15363 Planarity : 0.006 0.065 8630 Dihedral : 23.860 179.706 35066 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 3.44 % Allowed : 21.14 % Favored : 75.43 % 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: -0.66 (0.12), residues: 4788 helix: 0.82 (0.13), residues: 1561 sheet: -0.99 (0.17), residues: 890 loop : -1.04 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP h 17 HIS 0.029 0.002 HIS Q 79 PHE 0.031 0.003 PHE X 50 TYR 0.022 0.002 TYR L 12 ARG 0.010 0.001 ARG C 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22368.52 seconds wall clock time: 392 minutes 34.56 seconds (23554.56 seconds total)