Starting phenix.real_space_refine on Tue Feb 20 11:06:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekq_31173/02_2024/7ekq_31173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekq_31173/02_2024/7ekq_31173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekq_31173/02_2024/7ekq_31173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekq_31173/02_2024/7ekq_31173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekq_31173/02_2024/7ekq_31173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ekq_31173/02_2024/7ekq_31173.pdb" } resolution = 3.6 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= 0.021 sd= 0.138 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: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 17502 2.51 5 N 4719 2.21 5 O 5278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C ASP 49": "OD1" <-> "OD2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E ASP 49": "OD1" <-> "OD2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F ASP 203": "OD1" <-> "OD2" Residue "F PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G ASP 76": "OD1" <-> "OD2" Residue "G TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 132": "OD1" <-> "OD2" Residue "G ASP 165": "OD1" <-> "OD2" Residue "H ASP 367": "OD1" <-> "OD2" Residue "H GLU 404": "OE1" <-> "OE2" Residue "H GLU 430": "OE1" <-> "OE2" Residue "H TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 476": "OE1" <-> "OE2" Residue "H GLU 481": "OE1" <-> "OE2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "I ASP 27": "OD1" <-> "OD2" Residue "I ASP 62": "OD1" <-> "OD2" Residue "I TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 90": "OD1" <-> "OD2" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I ASP 181": "OD1" <-> "OD2" Residue "I GLU 203": "OE1" <-> "OE2" Residue "J PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 367": "OD1" <-> "OD2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J ASP 427": "OD1" <-> "OD2" Residue "J GLU 430": "OE1" <-> "OE2" Residue "J ASP 458": "OD1" <-> "OD2" Residue "J GLU 467": "OE1" <-> "OE2" Residue "K ASP 19": "OD1" <-> "OD2" Residue "K PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 145": "OD1" <-> "OD2" Residue "K ASP 147": "OD1" <-> "OD2" Residue "K TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 229": "OE1" <-> "OE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 103": "OD1" <-> "OD2" Residue "M GLU 414": "OE1" <-> "OE2" Residue "M GLU 430": "OE1" <-> "OE2" Residue "M ASP 437": "OD1" <-> "OD2" Residue "N GLU 42": "OE1" <-> "OE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N GLU 61": "OE1" <-> "OE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N GLU 146": "OE1" <-> "OE2" Residue "N ASP 156": "OD1" <-> "OD2" Residue "N TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 228": "OE1" <-> "OE2" Residue "N ASP 244": "OD1" <-> "OD2" Residue "N PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 331": "OD1" <-> "OD2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 62": "OD1" <-> "OD2" Residue "P PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "P GLU 87": "OE1" <-> "OE2" Residue "P PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 98": "OE1" <-> "OE2" Residue "Q ASP 99": "OD1" <-> "OD2" Residue "Q ASP 113": "OD1" <-> "OD2" Residue "Q ASP 166": "OD1" <-> "OD2" Residue "Q TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 193": "OE1" <-> "OE2" Residue "Q PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 16": "OD1" <-> "OD2" Residue "R GLU 25": "OE1" <-> "OE2" Residue "R TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R GLU 116": "OE1" <-> "OE2" Residue "R PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 149": "OE1" <-> "OE2" Residue "R TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 179": "OD1" <-> "OD2" Residue "S PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 16": "OD1" <-> "OD2" Residue "S TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 86": "OE1" <-> "OE2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S GLU 146": "OE1" <-> "OE2" Residue "S TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 188": "OD1" <-> "OD2" 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: 27663 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1763 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "B" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1477 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain: "C" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1329 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1477 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 7, 'TRANS': 185} Chain: "E" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1329 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "F" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1307 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 5, 'TRANS': 166} Chain: "G" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1369 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "H" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1131 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "I" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1745 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "J" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1279 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain: "K" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1841 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 217} Chain: "L" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1494 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain: "M" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1014 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "N" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2691 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 23, 'TRANS': 314} Chain: "O" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1259 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "P" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 713 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "Q" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1567 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 188} Chain breaks: 1 Chain: "R" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1439 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 184} Chain: "S" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1439 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 184} Time building chain proxies: 14.42, per 1000 atoms: 0.52 Number of scatterers: 27663 At special positions: 0 Unit cell: (166.068, 163.432, 127.846, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 164 16.00 O 5278 8.00 N 4719 7.00 C 17502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.13 Conformation dependent library (CDL) restraints added in 4.8 seconds 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6574 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 47 sheets defined 40.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.975A pdb=" N THR A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.834A pdb=" N VAL A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 118 removed outlier: 3.802A pdb=" N VAL A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 170 removed outlier: 3.685A pdb=" N ALA A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.541A pdb=" N ILE A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.968A pdb=" N LEU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'B' and resid 43 through 58 removed outlier: 3.852A pdb=" N ILE B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 58 " --> pdb=" O VAL B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 removed outlier: 3.507A pdb=" N ASN B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 87 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.713A pdb=" N GLY B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 139 Processing helix chain 'B' and resid 165 through 192 removed outlier: 3.861A pdb=" N GLU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.606A pdb=" N THR B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.854A pdb=" N ILE B 214 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.838A pdb=" N ARG C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 52 removed outlier: 3.575A pdb=" N ASP C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 80 removed outlier: 4.268A pdb=" N GLY C 73 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 103 removed outlier: 3.579A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 152 removed outlier: 3.680A pdb=" N ILE C 133 " --> pdb=" O GLN C 129 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 135 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 140 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 removed outlier: 3.744A pdb=" N GLU C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 removed outlier: 4.142A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 59 removed outlier: 4.340A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 removed outlier: 3.598A pdb=" N ASN D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 76 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 115 removed outlier: 3.521A pdb=" N ALA D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 115 " --> pdb=" O PHE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 165 through 192 removed outlier: 3.773A pdb=" N GLU D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 202 removed outlier: 3.771A pdb=" N ILE D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 199 " --> pdb=" O MET D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 removed outlier: 4.689A pdb=" N GLU D 215 " --> pdb=" O GLN D 211 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 24 Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.603A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 48 " --> pdb=" O GLN E 44 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.916A pdb=" N ILE E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR E 75 " --> pdb=" O GLY E 71 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 3.743A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 152 removed outlier: 3.514A pdb=" N GLU E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 166 removed outlier: 3.567A pdb=" N GLU E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR E 166 " --> pdb=" O ILE E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 removed outlier: 3.577A pdb=" N LYS E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU E 179 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 4.159A pdb=" N GLN F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 60' Processing helix chain 'F' and resid 70 through 88 removed outlier: 3.720A pdb=" N TYR F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP F 85 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 86 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 116 removed outlier: 3.673A pdb=" N GLY F 107 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP F 112 " --> pdb=" O MET F 108 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET F 114 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG F 115 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 139 removed outlier: 3.749A pdb=" N ILE F 136 " --> pdb=" O MET F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 192 removed outlier: 3.749A pdb=" N GLU F 170 " --> pdb=" O ALA F 166 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 171 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU F 175 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 189 " --> pdb=" O GLY F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 removed outlier: 3.898A pdb=" N ILE F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR F 199 " --> pdb=" O MET F 195 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 202 " --> pdb=" O ILE F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 217 removed outlier: 4.391A pdb=" N GLU F 215 " --> pdb=" O GLN F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 24 removed outlier: 3.504A pdb=" N ARG G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 52 removed outlier: 3.947A pdb=" N ASP G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA G 40 " --> pdb=" O PHE G 36 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G 48 " --> pdb=" O GLN G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 81 removed outlier: 3.666A pdb=" N MET G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY G 73 " --> pdb=" O THR G 69 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 103 removed outlier: 3.673A pdb=" N GLY G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA G 103 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 152 removed outlier: 3.743A pdb=" N GLU G 134 " --> pdb=" O ALA G 130 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE G 135 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 166 removed outlier: 4.003A pdb=" N GLU G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR G 166 " --> pdb=" O ILE G 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 370 removed outlier: 3.709A pdb=" N GLY H 362 " --> pdb=" O SER H 358 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR H 364 " --> pdb=" O GLY H 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL H 365 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN H 370 " --> pdb=" O HIS H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 394 Processing helix chain 'H' and resid 420 through 446 removed outlier: 3.862A pdb=" N ILE H 424 " --> pdb=" O GLN H 420 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE H 426 " --> pdb=" O SER H 422 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP H 427 " --> pdb=" O ASP H 423 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 429 " --> pdb=" O TRP H 425 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE H 441 " --> pdb=" O ASP H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 457 removed outlier: 3.651A pdb=" N LEU H 454 " --> pdb=" O ARG H 450 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG H 455 " --> pdb=" O HIS H 451 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP H 456 " --> pdb=" O LYS H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 472 removed outlier: 3.572A pdb=" N THR H 468 " --> pdb=" O THR H 464 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE H 469 " --> pdb=" O ALA H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 490 removed outlier: 3.640A pdb=" N SER H 485 " --> pdb=" O GLU H 481 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE H 486 " --> pdb=" O VAL H 482 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU H 488 " --> pdb=" O HIS H 484 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR H 490 " --> pdb=" O ILE H 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 35 Processing helix chain 'I' and resid 48 through 60 removed outlier: 3.906A pdb=" N VAL I 52 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 101 removed outlier: 3.859A pdb=" N ALA I 95 " --> pdb=" O ASN I 91 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 124 removed outlier: 3.646A pdb=" N LEU I 122 " --> pdb=" O GLN I 118 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 179 removed outlier: 3.508A pdb=" N GLN I 157 " --> pdb=" O ALA I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 189 removed outlier: 3.670A pdb=" N CYS I 185 " --> pdb=" O ASP I 181 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN I 186 " --> pdb=" O LEU I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 205 removed outlier: 3.721A pdb=" N TYR I 202 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU I 203 " --> pdb=" O LYS I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'J' and resid 358 through 368 removed outlier: 3.852A pdb=" N GLY J 362 " --> pdb=" O SER J 358 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE J 363 " --> pdb=" O VAL J 359 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 394 removed outlier: 4.055A pdb=" N LEU J 390 " --> pdb=" O SER J 386 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA J 391 " --> pdb=" O ALA J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 446 removed outlier: 4.091A pdb=" N ILE J 426 " --> pdb=" O SER J 422 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP J 427 " --> pdb=" O ASP J 423 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER J 428 " --> pdb=" O ILE J 424 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU J 430 " --> pdb=" O ILE J 426 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR J 446 " --> pdb=" O TYR J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 455 removed outlier: 3.643A pdb=" N ILE J 453 " --> pdb=" O PRO J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 472 removed outlier: 3.692A pdb=" N ILE J 469 " --> pdb=" O ALA J 465 " (cutoff:3.500A) Processing helix chain 'J' and resid 479 through 509 removed outlier: 3.696A pdb=" N HIS J 484 " --> pdb=" O ASN J 480 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER J 485 " --> pdb=" O GLU J 481 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN J 492 " --> pdb=" O GLU J 488 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL J 493 " --> pdb=" O MET J 489 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP J 494 " --> pdb=" O THR J 490 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS J 497 " --> pdb=" O VAL J 493 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS J 500 " --> pdb=" O TYR J 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 removed outlier: 3.503A pdb=" N LEU K 10 " --> pdb=" O LEU K 6 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP K 11 " --> pdb=" O ARG K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 27 removed outlier: 3.733A pdb=" N ARG K 23 " --> pdb=" O ASP K 19 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU K 27 " --> pdb=" O ARG K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.950A pdb=" N GLU K 42 " --> pdb=" O SER K 38 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU K 54 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.526A pdb=" N MET K 88 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 111 Processing helix chain 'K' and resid 145 through 169 removed outlier: 3.601A pdb=" N LYS K 151 " --> pdb=" O ASP K 147 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR K 157 " --> pdb=" O THR K 153 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS K 167 " --> pdb=" O TYR K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 178 removed outlier: 3.766A pdb=" N ILE K 175 " --> pdb=" O THR K 171 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET K 176 " --> pdb=" O GLU K 172 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP K 178 " --> pdb=" O GLN K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 194 Processing helix chain 'K' and resid 210 through 214 removed outlier: 3.919A pdb=" N LYS K 214 " --> pdb=" O ASP K 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 61 Processing helix chain 'L' and resid 71 through 89 removed outlier: 3.557A pdb=" N ASN L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN L 77 " --> pdb=" O ASP L 73 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU L 83 " --> pdb=" O ILE L 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 117 removed outlier: 3.522A pdb=" N LEU L 110 " --> pdb=" O PRO L 106 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR L 113 " --> pdb=" O ALA L 109 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET L 114 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN L 115 " --> pdb=" O TYR L 111 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL L 117 " --> pdb=" O THR L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 134 removed outlier: 3.511A pdb=" N GLY L 134 " --> pdb=" O GLY L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 Processing helix chain 'L' and resid 166 through 193 removed outlier: 3.671A pdb=" N HIS L 171 " --> pdb=" O ALA L 167 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE L 172 " --> pdb=" O SER L 168 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR L 183 " --> pdb=" O ARG L 179 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR L 188 " --> pdb=" O LEU L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 203 removed outlier: 3.611A pdb=" N VAL L 199 " --> pdb=" O PRO L 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE L 200 " --> pdb=" O TYR L 196 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG L 201 " --> pdb=" O ASP L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 217 removed outlier: 4.230A pdb=" N GLU L 216 " --> pdb=" O LYS L 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 371 removed outlier: 3.693A pdb=" N THR M 364 " --> pdb=" O GLY M 360 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU M 369 " --> pdb=" O VAL M 365 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN M 370 " --> pdb=" O HIS M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 394 removed outlier: 3.591A pdb=" N LEU M 390 " --> pdb=" O SER M 386 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 447 removed outlier: 3.923A pdb=" N ILE M 424 " --> pdb=" O GLN M 420 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TRP M 425 " --> pdb=" O ALA M 421 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN M 429 " --> pdb=" O TRP M 425 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU M 444 " --> pdb=" O GLU M 440 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER M 445 " --> pdb=" O ILE M 441 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR M 447 " --> pdb=" O SER M 443 " (cutoff:3.500A) Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.874A pdb=" N ILE M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG M 455 " --> pdb=" O HIS M 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 466 through 471 removed outlier: 3.868A pdb=" N TYR M 470 " --> pdb=" O MET M 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 27 removed outlier: 3.582A pdb=" N GLN N 27 " --> pdb=" O LEU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 54 removed outlier: 3.852A pdb=" N GLU N 42 " --> pdb=" O PRO N 38 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN N 54 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 93 removed outlier: 3.568A pdb=" N ALA N 85 " --> pdb=" O SER N 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR N 87 " --> pdb=" O GLY N 83 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR N 89 " --> pdb=" O ALA N 85 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET N 90 " --> pdb=" O LEU N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 115 Processing helix chain 'N' and resid 144 through 170 removed outlier: 4.076A pdb=" N HIS N 148 " --> pdb=" O ALA N 144 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 149 " --> pdb=" O ILE N 145 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY N 168 " --> pdb=" O MET N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 180 removed outlier: 3.789A pdb=" N ALA N 178 " --> pdb=" O ASP N 174 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP N 179 " --> pdb=" O LYS N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 195 Processing helix chain 'N' and resid 204 through 218 removed outlier: 3.661A pdb=" N TRP N 215 " --> pdb=" O ALA N 211 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE N 216 " --> pdb=" O ALA N 212 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 224 removed outlier: 4.232A pdb=" N GLU N 224 " --> pdb=" O ARG N 220 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 263 removed outlier: 3.631A pdb=" N GLN N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU N 232 " --> pdb=" O GLU N 228 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP N 244 " --> pdb=" O TYR N 240 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER N 245 " --> pdb=" O ALA N 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET N 250 " --> pdb=" O PHE N 246 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR N 251 " --> pdb=" O ARG N 247 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 277 removed outlier: 4.011A pdb=" N MET N 273 " --> pdb=" O SER N 269 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU N 274 " --> pdb=" O SER N 270 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN N 275 " --> pdb=" O ARG N 271 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL N 276 " --> pdb=" O ASN N 272 " (cutoff:3.500A) Processing helix chain 'O' and resid 1 through 6 removed outlier: 4.269A pdb=" N THR O 4 " --> pdb=" O ALA O 1 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA O 6 " --> pdb=" O ALA O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 12 Processing helix chain 'O' and resid 16 through 33 removed outlier: 3.593A pdb=" N SER O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE O 23 " --> pdb=" O ALA O 19 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE O 29 " --> pdb=" O TYR O 25 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 50 removed outlier: 3.731A pdb=" N GLY O 46 " --> pdb=" O MET O 42 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE O 47 " --> pdb=" O VAL O 43 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU O 48 " --> pdb=" O LEU O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.739A pdb=" N LEU O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER O 61 " --> pdb=" O LYS O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 81 removed outlier: 3.790A pdb=" N ALA O 70 " --> pdb=" O ASP O 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL O 74 " --> pdb=" O ALA O 70 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU O 75 " --> pdb=" O TRP O 71 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN O 79 " --> pdb=" O LEU O 75 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL O 80 " --> pdb=" O TRP O 76 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 114 removed outlier: 3.812A pdb=" N LYS O 101 " --> pdb=" O ASP O 97 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL O 102 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE O 103 " --> pdb=" O ALA O 99 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL O 111 " --> pdb=" O SER O 107 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 131 removed outlier: 3.890A pdb=" N VAL O 123 " --> pdb=" O TYR O 119 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU O 124 " --> pdb=" O SER O 120 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY O 131 " --> pdb=" O LEU O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 137 removed outlier: 3.811A pdb=" N ASP O 135 " --> pdb=" O GLY O 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU O 136 " --> pdb=" O VAL O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 156 removed outlier: 3.547A pdb=" N VAL O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL O 151 " --> pdb=" O VAL O 147 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU O 152 " --> pdb=" O ARG O 148 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS O 153 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 38 removed outlier: 3.550A pdb=" N GLY P 36 " --> pdb=" O LYS P 33 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY P 37 " --> pdb=" O THR P 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 removed outlier: 4.426A pdb=" N LYS R 28 " --> pdb=" O GLU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 101 removed outlier: 3.642A pdb=" N GLN R 100 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 101 removed outlier: 3.518A pdb=" N GLN S 100 " --> pdb=" O LYS S 97 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU S 101 " --> pdb=" O ILE S 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 97 through 101' Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 removed outlier: 6.245A pdb=" N ILE A 42 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASN A 77 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE A 44 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 72 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL A 103 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU A 105 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 76 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALA A 107 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 78 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR A 125 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR A 102 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.262A pdb=" N HIS A 185 " --> pdb=" O MET A 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 66 removed outlier: 6.611A pdb=" N VAL B 63 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN B 98 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 65 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N TYR B 146 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR B 123 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.104A pdb=" N ILE C 57 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR C 88 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE C 59 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE C 61 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU C 92 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 94 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG C 116 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY C 91 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N MET C 118 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 93 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 170 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.104A pdb=" N ILE C 57 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR C 88 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE C 59 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE C 61 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU C 92 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 94 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASN C 110 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR C 87 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER C 111 " --> pdb=" O HIS C 185 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 64 removed outlier: 6.335A pdb=" N VAL D 63 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASN D 98 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU D 128 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D 206 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 62 through 64 removed outlier: 6.335A pdb=" N VAL D 63 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASN D 98 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU D 128 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYR D 146 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR D 123 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 160 through 164 removed outlier: 3.666A pdb=" N GLY D 160 " --> pdb=" O GLY M 419 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY D 164 " --> pdb=" O GLY M 415 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY M 415 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 26 through 30 removed outlier: 6.289A pdb=" N VAL E 27 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASN E 62 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU E 29 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE E 57 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TYR E 88 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE E 59 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE E 61 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU E 92 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG E 116 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLY E 91 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET E 118 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA E 93 " --> pdb=" O MET E 118 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 170 " --> pdb=" O ILE E 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 26 through 30 removed outlier: 6.289A pdb=" N VAL E 27 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASN E 62 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU E 29 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE E 57 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N TYR E 88 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE E 59 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE E 61 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU E 92 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASN E 110 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR E 87 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 62 through 66 removed outlier: 7.184A pdb=" N VAL F 63 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASN F 98 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU F 65 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N MET F 95 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 126 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL F 97 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU F 128 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR F 123 " --> pdb=" O TYR F 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 62 through 66 removed outlier: 7.184A pdb=" N VAL F 63 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASN F 98 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU F 65 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N MET F 95 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 126 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL F 97 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU F 128 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG F 152 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY F 127 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N MET F 154 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA F 129 " --> pdb=" O MET F 154 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 206 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 26 through 30 removed outlier: 6.114A pdb=" N ILE G 57 " --> pdb=" O ASN G 86 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR G 88 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE G 59 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE G 61 " --> pdb=" O PHE G 90 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU G 92 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASN G 110 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N THR G 87 " --> pdb=" O ASN G 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'G' and resid 124 through 126 removed outlier: 4.451A pdb=" N GLY G 124 " --> pdb=" O GLY J 419 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY J 419 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA G 126 " --> pdb=" O LEU J 417 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J 417 " --> pdb=" O ALA G 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 347 through 352 removed outlier: 3.653A pdb=" N MET H 350 " --> pdb=" O LEU H 377 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU H 379 " --> pdb=" O MET H 350 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL H 402 " --> pdb=" O GLU H 476 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 408 through 410 Processing sheet with id=AC3, first strand: chain 'I' and resid 37 through 40 removed outlier: 5.861A pdb=" N ILE I 70 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLY I 110 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL I 72 " --> pdb=" O GLY I 110 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR I 112 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N LEU I 74 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS I 114 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER I 76 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TYR I 132 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR I 109 " --> pdb=" O TYR I 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 139 through 141 removed outlier: 3.776A pdb=" N THR I 141 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG I 194 " --> pdb=" O THR I 141 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 348 through 352 removed outlier: 3.722A pdb=" N THR J 403 " --> pdb=" O ALA J 380 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG J 400 " --> pdb=" O GLU J 476 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA J 478 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL J 402 " --> pdb=" O ALA J 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 383 through 384 removed outlier: 6.115A pdb=" N ALA J 384 " --> pdb=" O MET J 409 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE J 410 " --> pdb=" O PHE J 461 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE J 461 " --> pdb=" O ILE J 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'K' and resid 29 through 32 removed outlier: 5.317A pdb=" N SER K 65 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN K 104 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N MET K 130 " --> pdb=" O GLY K 103 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA K 105 " --> pdb=" O MET K 130 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE K 129 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 29 through 32 removed outlier: 5.317A pdb=" N SER K 65 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN K 104 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALA K 122 " --> pdb=" O ILE K 97 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR K 99 " --> pdb=" O ALA K 122 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG K 121 " --> pdb=" O THR K 198 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AD1, first strand: chain 'L' and resid 63 through 66 removed outlier: 5.879A pdb=" N ILE L 93 " --> pdb=" O ALA L 122 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR L 95 " --> pdb=" O VAL L 124 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 128 through 129 removed outlier: 3.520A pdb=" N MET L 155 " --> pdb=" O CYS L 129 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS L 207 " --> pdb=" O MET L 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 348 through 354 removed outlier: 6.586A pdb=" N VAL M 348 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU M 379 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET M 350 " --> pdb=" O LEU M 379 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU M 381 " --> pdb=" O MET M 350 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE M 352 " --> pdb=" O LEU M 381 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL M 383 " --> pdb=" O ILE M 352 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N HIS M 407 " --> pdb=" O ALA M 380 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY M 382 " --> pdb=" O HIS M 407 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N MET M 409 " --> pdb=" O GLY M 382 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA M 384 " --> pdb=" O MET M 409 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 348 through 354 removed outlier: 6.586A pdb=" N VAL M 348 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU M 379 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET M 350 " --> pdb=" O LEU M 379 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LEU M 381 " --> pdb=" O MET M 350 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE M 352 " --> pdb=" O LEU M 381 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL M 383 " --> pdb=" O ILE M 352 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR M 401 " --> pdb=" O SER M 376 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR M 378 " --> pdb=" O TYR M 401 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU M 476 " --> pdb=" O ARG M 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL M 402 " --> pdb=" O GLU M 476 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 29 through 32 removed outlier: 5.857A pdb=" N ILE N 60 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL N 100 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N MET N 62 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET N 102 " --> pdb=" O MET N 62 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE N 64 " --> pdb=" O MET N 102 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU N 104 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER N 66 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL N 106 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU N 128 " --> pdb=" O ASN N 101 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLY N 103 " --> pdb=" O LEU N 128 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N MET N 130 " --> pdb=" O GLY N 103 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA N 105 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE N 131 " --> pdb=" O LEU N 184 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 32 removed outlier: 5.857A pdb=" N ILE N 60 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL N 100 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N MET N 62 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N MET N 102 " --> pdb=" O MET N 62 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE N 64 " --> pdb=" O MET N 102 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU N 104 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER N 66 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL N 106 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LYS N 122 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR N 99 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER N 123 " --> pdb=" O GLU N 199 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 37 through 38 Processing sheet with id=AD8, first strand: chain 'P' and resid 72 through 73 removed outlier: 3.717A pdb=" N VAL P 73 " --> pdb=" O ALA P 51 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA P 51 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS P 52 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU P 24 " --> pdb=" O GLY P 54 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL P 23 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL P 93 " --> pdb=" O VAL P 23 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE P 25 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE P 91 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY P 88 " --> pdb=" O VAL P 85 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 2 through 4 removed outlier: 6.720A pdb=" N ILE Q 3 " --> pdb=" O LYS Q 86 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN Q 83 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU Q 20 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 103 through 104 Processing sheet with id=AE2, first strand: chain 'Q' and resid 181 through 184 removed outlier: 7.003A pdb=" N LEU Q 126 " --> pdb=" O VAL Q 156 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL Q 158 " --> pdb=" O ARG Q 124 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ARG Q 124 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS Q 199 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 160 through 163 removed outlier: 3.994A pdb=" N LYS Q 162 " --> pdb=" O ARG Q 172 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 12 through 13 removed outlier: 3.501A pdb=" N LYS R 12 " --> pdb=" O GLN S 192 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 17 through 21 removed outlier: 3.894A pdb=" N THR R 71 " --> pdb=" O LEU R 82 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 62 through 65 removed outlier: 4.130A pdb=" N LYS R 62 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY R 90 " --> pdb=" O ILE R 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 163 through 164 removed outlier: 4.231A pdb=" N ALA R 140 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU R 109 " --> pdb=" O ALA R 140 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 145 through 146 Processing sheet with id=AE9, first strand: chain 'S' and resid 48 through 50 removed outlier: 6.124A pdb=" N ILE S 48 " --> pdb=" O LYS S 21 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS S 21 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA S 50 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR S 71 " --> pdb=" O LEU S 82 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 138 through 141 removed outlier: 3.572A pdb=" N VAL S 139 " --> pdb=" O LEU S 109 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU S 109 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR S 172 " --> pdb=" O VAL S 183 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.745A pdb=" N ALA S 152 " --> pdb=" O ASP S 147 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2661 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.58 Time building geometry restraints manager: 11.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9212 1.35 - 1.46: 5924 1.46 - 1.58: 12720 1.58 - 1.70: 0 1.70 - 1.82: 293 Bond restraints: 28149 Sorted by residual: bond pdb=" CA THR O 35 " pdb=" CB THR O 35 " ideal model delta sigma weight residual 1.530 1.575 -0.045 1.57e-02 4.06e+03 8.32e+00 bond pdb=" N SER S 187 " pdb=" CA SER S 187 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.97e+00 bond pdb=" C PRO Q 37 " pdb=" N PRO Q 38 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.61e+00 bond pdb=" C GLU S 186 " pdb=" N SER S 187 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.40e-02 5.10e+03 4.25e+00 bond pdb=" C GLU R 186 " pdb=" N SER R 187 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.40e-02 5.10e+03 4.24e+00 ... (remaining 28144 not shown) Histogram of bond angle deviations from ideal: 99.92 - 107.75: 1040 107.75 - 115.59: 17180 115.59 - 123.43: 19042 123.43 - 131.26: 740 131.26 - 139.10: 41 Bond angle restraints: 38043 Sorted by residual: angle pdb=" C GLU R 186 " pdb=" N SER R 187 " pdb=" CA SER R 187 " ideal model delta sigma weight residual 121.70 139.10 -17.40 1.80e+00 3.09e-01 9.34e+01 angle pdb=" C GLU S 186 " pdb=" N SER S 187 " pdb=" CA SER S 187 " ideal model delta sigma weight residual 121.70 137.08 -15.38 1.80e+00 3.09e-01 7.30e+01 angle pdb=" C VAL R 33 " pdb=" N LEU R 34 " pdb=" CA LEU R 34 " ideal model delta sigma weight residual 121.54 131.41 -9.87 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C LYS S 168 " pdb=" N TYR S 169 " pdb=" CA TYR S 169 " ideal model delta sigma weight residual 122.61 129.77 -7.16 1.56e+00 4.11e-01 2.11e+01 angle pdb=" C LYS P 86 " pdb=" N GLU P 87 " pdb=" CA GLU P 87 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 ... (remaining 38038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 15520 17.12 - 34.24: 1259 34.24 - 51.35: 303 51.35 - 68.47: 42 68.47 - 85.59: 16 Dihedral angle restraints: 17140 sinusoidal: 6868 harmonic: 10272 Sorted by residual: dihedral pdb=" CA GLU S 186 " pdb=" C GLU S 186 " pdb=" N SER S 187 " pdb=" CA SER S 187 " ideal model delta harmonic sigma weight residual 0.00 39.18 -39.18 0 5.00e+00 4.00e-02 6.14e+01 dihedral pdb=" CA GLU R 186 " pdb=" C GLU R 186 " pdb=" N SER R 187 " pdb=" CA SER R 187 " ideal model delta harmonic sigma weight residual 0.00 32.29 -32.29 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA LEU R 34 " pdb=" C LEU R 34 " pdb=" N LEU R 35 " pdb=" CA LEU R 35 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 17137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3298 0.049 - 0.098: 734 0.098 - 0.147: 230 0.147 - 0.195: 18 0.195 - 0.244: 7 Chirality restraints: 4287 Sorted by residual: chirality pdb=" CB VAL N 327 " pdb=" CA VAL N 327 " pdb=" CG1 VAL N 327 " pdb=" CG2 VAL N 327 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LEU K 135 " pdb=" N LEU K 135 " pdb=" C LEU K 135 " pdb=" CB LEU K 135 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL S 123 " pdb=" CA VAL S 123 " pdb=" CG1 VAL S 123 " pdb=" CG2 VAL S 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 4284 not shown) Planarity restraints: 4940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 16 " -0.053 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO K 17 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO K 17 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO K 17 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 43 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO Q 44 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO Q 44 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO Q 44 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 118 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO F 119 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 119 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 119 " 0.031 5.00e-02 4.00e+02 ... (remaining 4937 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7712 2.80 - 3.33: 22795 3.33 - 3.85: 44561 3.85 - 4.38: 50569 4.38 - 4.90: 85203 Nonbonded interactions: 210840 Sorted by model distance: nonbonded pdb=" O THR M 464 " pdb=" OG1 THR M 468 " model vdw 2.280 2.440 nonbonded pdb=" O ASP I 27 " pdb=" OG SER I 30 " model vdw 2.285 2.440 nonbonded pdb=" O THR H 464 " pdb=" OG1 THR H 468 " model vdw 2.292 2.440 nonbonded pdb=" O PHE D 135 " pdb=" OG SER D 139 " model vdw 2.308 2.440 nonbonded pdb=" O ALA M 439 " pdb=" OG SER M 443 " model vdw 2.320 2.440 ... (remaining 210835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 54 through 225) selection = (chain 'D' and resid 54 through 225) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'E' selection = (chain 'G' and resid 17 through 190) } ncs_group { reference = (chain 'H' and resid 346 through 478) selection = (chain 'J' and resid 346 through 478) selection = chain 'M' } ncs_group { reference = chain 'R' selection = chain 'S' } 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 group one per residue 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.570 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 67.350 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 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 : 0.003 0.050 28149 Z= 0.180 Angle : 0.707 17.398 38043 Z= 0.386 Chirality : 0.046 0.244 4287 Planarity : 0.006 0.078 4940 Dihedral : 13.219 85.589 10566 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.14 % Allowed : 6.76 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.10), residues: 3543 helix: -4.88 (0.04), residues: 1341 sheet: -0.91 (0.22), residues: 467 loop : -2.65 (0.11), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 96 HIS 0.014 0.001 HIS O 113 PHE 0.015 0.001 PHE P 92 TYR 0.011 0.001 TYR S 166 ARG 0.003 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1172 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7685 (p0) cc_final: 0.7484 (p0) REVERT: A 51 LYS cc_start: 0.8747 (tppt) cc_final: 0.8321 (tptp) REVERT: A 64 GLU cc_start: 0.7213 (tp30) cc_final: 0.6681 (tp30) REVERT: A 78 SER cc_start: 0.8823 (p) cc_final: 0.8592 (t) REVERT: A 156 ASN cc_start: 0.7982 (m110) cc_final: 0.7412 (t0) REVERT: A 164 ARG cc_start: 0.5721 (mtp180) cc_final: 0.5183 (mtp85) REVERT: A 172 MET cc_start: 0.5834 (ptm) cc_final: 0.5255 (ptm) REVERT: A 187 MET cc_start: 0.6502 (mpp) cc_final: 0.6120 (mtm) REVERT: A 214 ILE cc_start: 0.8689 (mm) cc_final: 0.8317 (mm) REVERT: B 76 LEU cc_start: 0.9194 (mm) cc_final: 0.8584 (mp) REVERT: B 167 THR cc_start: 0.7880 (p) cc_final: 0.7253 (m) REVERT: B 200 LYS cc_start: 0.8661 (tppt) cc_final: 0.8115 (tptt) REVERT: C 47 LEU cc_start: 0.8615 (mm) cc_final: 0.8214 (mm) REVERT: C 48 LEU cc_start: 0.8952 (mm) cc_final: 0.8480 (mm) REVERT: C 72 MET cc_start: 0.8326 (tpt) cc_final: 0.7763 (tpp) REVERT: C 74 ILE cc_start: 0.8961 (mt) cc_final: 0.7932 (mm) REVERT: C 159 LEU cc_start: 0.6835 (tp) cc_final: 0.6102 (pp) REVERT: C 165 ASP cc_start: 0.8159 (m-30) cc_final: 0.7636 (m-30) REVERT: C 167 ASP cc_start: 0.8640 (p0) cc_final: 0.8353 (p0) REVERT: C 175 LEU cc_start: 0.7935 (tp) cc_final: 0.6915 (tp) REVERT: C 180 TYR cc_start: 0.5015 (t80) cc_final: 0.4801 (t80) REVERT: D 165 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8000 (mt0) REVERT: D 168 ASP cc_start: 0.7850 (t0) cc_final: 0.7471 (t0) REVERT: E 34 GLU cc_start: 0.7318 (pt0) cc_final: 0.6981 (mm-30) REVERT: E 74 ILE cc_start: 0.8443 (mp) cc_final: 0.7690 (mp) REVERT: E 82 ARG cc_start: 0.7157 (ptt-90) cc_final: 0.6054 (ptt180) REVERT: E 84 ASP cc_start: 0.7168 (m-30) cc_final: 0.6954 (m-30) REVERT: E 164 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7753 (mm-30) REVERT: F 110 VAL cc_start: 0.9304 (m) cc_final: 0.9053 (t) REVERT: F 154 MET cc_start: 0.7365 (tmm) cc_final: 0.6384 (ttt) REVERT: F 195 MET cc_start: 0.7212 (tpt) cc_final: 0.6875 (tpp) REVERT: G 146 ASN cc_start: 0.7653 (t0) cc_final: 0.6951 (t0) REVERT: H 352 ILE cc_start: 0.8738 (mm) cc_final: 0.8519 (mt) REVERT: H 425 TRP cc_start: 0.8022 (t-100) cc_final: 0.7147 (t-100) REVERT: H 451 HIS cc_start: 0.7031 (p-80) cc_final: 0.6711 (p-80) REVERT: H 471 TYR cc_start: 0.7510 (t80) cc_final: 0.6724 (t80) REVERT: I 80 ILE cc_start: 0.8560 (mm) cc_final: 0.8179 (pt) REVERT: I 102 PHE cc_start: 0.3219 (t80) cc_final: 0.1392 (t80) REVERT: I 147 ASN cc_start: 0.8052 (p0) cc_final: 0.7659 (p0) REVERT: J 371 PHE cc_start: 0.5939 (p90) cc_final: 0.5679 (p90) REVERT: J 411 HIS cc_start: 0.7346 (t70) cc_final: 0.7140 (t70) REVERT: J 425 TRP cc_start: 0.7312 (t60) cc_final: 0.6977 (t-100) REVERT: J 429 GLN cc_start: 0.7919 (mm110) cc_final: 0.7631 (mm-40) REVERT: J 432 MET cc_start: 0.8200 (mmp) cc_final: 0.7207 (mmm) REVERT: J 436 LEU cc_start: 0.7094 (tt) cc_final: 0.6756 (mt) REVERT: K 64 ASN cc_start: 0.6728 (t0) cc_final: 0.6411 (t0) REVERT: K 150 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7150 (ttm170) REVERT: K 215 MET cc_start: 0.5657 (ppp) cc_final: 0.4588 (mmm) REVERT: L 111 TYR cc_start: 0.7902 (t80) cc_final: 0.7448 (t80) REVERT: L 155 MET cc_start: 0.7566 (tpt) cc_final: 0.7236 (tpt) REVERT: L 169 GLU cc_start: 0.8060 (pp20) cc_final: 0.7558 (pt0) REVERT: L 200 ILE cc_start: 0.7637 (mm) cc_final: 0.7406 (tp) REVERT: M 414 GLU cc_start: 0.7784 (pp20) cc_final: 0.7414 (pm20) REVERT: M 417 LEU cc_start: 0.8658 (mp) cc_final: 0.7748 (mt) REVERT: M 420 GLN cc_start: 0.6786 (tm-30) cc_final: 0.6239 (tt0) REVERT: M 431 ILE cc_start: 0.8513 (mm) cc_final: 0.8137 (mm) REVERT: N 19 ASP cc_start: 0.7728 (p0) cc_final: 0.7330 (p0) REVERT: N 152 ARG cc_start: 0.7636 (mmt180) cc_final: 0.7367 (mmm-85) REVERT: N 160 GLU cc_start: 0.6774 (tp30) cc_final: 0.6116 (tp30) REVERT: N 180 MET cc_start: 0.7487 (ttp) cc_final: 0.7258 (ttp) REVERT: N 181 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7568 (mm-40) REVERT: N 185 TYR cc_start: 0.8388 (m-80) cc_final: 0.8011 (m-80) REVERT: N 291 ASN cc_start: 0.7691 (m-40) cc_final: 0.6746 (p0) REVERT: O 45 MET cc_start: 0.7829 (tpp) cc_final: 0.7618 (tpp) REVERT: P 40 LEU cc_start: 0.5782 (tp) cc_final: 0.5290 (tp) REVERT: Q 85 LEU cc_start: 0.6181 (tp) cc_final: 0.5507 (tp) REVERT: Q 163 TYR cc_start: 0.2441 (t80) cc_final: 0.1964 (t80) REVERT: R 166 TYR cc_start: 0.4770 (p90) cc_final: 0.4441 (p90) REVERT: S 19 LEU cc_start: 0.4559 (tp) cc_final: 0.4335 (tp) REVERT: S 180 ASN cc_start: 0.5540 (p0) cc_final: 0.5294 (p0) outliers start: 4 outliers final: 0 residues processed: 1176 average time/residue: 0.4100 time to fit residues: 723.0757 Evaluate side-chains 711 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 711 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 8.9990 chunk 264 optimal weight: 0.0570 chunk 146 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 273 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 overall best weight: 3.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 136 GLN A 156 ASN A 176 GLN A 191 GLN A 217 GLN B 89 ASN B 172 GLN B 178 HIS C 51 GLN C 146 ASN C 148 ASN C 185 HIS D 172 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 60 GLN F 116 HIS F 150 ASN F 156 HIS F 157 GLN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 HIS G 24 GLN G 44 GLN G 136 GLN G 146 ASN G 156 GLN ** H 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 491 ASN I 55 GLN ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN J 361 ASN ** J 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 420 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN ** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 GLN K 230 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 ASN ** M 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 HIS ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 28149 Z= 0.365 Angle : 0.794 14.822 38043 Z= 0.412 Chirality : 0.048 0.264 4287 Planarity : 0.006 0.078 4940 Dihedral : 4.979 48.818 3885 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 4.05 % Allowed : 17.09 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.16 (0.12), residues: 3543 helix: -2.57 (0.10), residues: 1402 sheet: -0.54 (0.23), residues: 498 loop : -2.07 (0.13), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP O 112 HIS 0.012 0.002 HIS I 136 PHE 0.025 0.003 PHE S 174 TYR 0.031 0.002 TYR K 163 ARG 0.007 0.001 ARG I 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 774 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8879 (tppt) cc_final: 0.8537 (tptt) REVERT: A 136 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: A 174 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: A 176 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: A 188 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8084 (m) REVERT: B 104 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8904 (t) REVERT: C 23 ARG cc_start: 0.8241 (mtm110) cc_final: 0.7966 (mtm180) REVERT: C 74 ILE cc_start: 0.8852 (mt) cc_final: 0.8612 (mt) REVERT: C 110 ASN cc_start: 0.6941 (m-40) cc_final: 0.6639 (m-40) REVERT: C 127 SER cc_start: 0.8734 (t) cc_final: 0.8440 (p) REVERT: C 144 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8038 (mtmm) REVERT: D 83 TYR cc_start: 0.8280 (t80) cc_final: 0.7683 (t80) REVERT: D 96 TYR cc_start: 0.7833 (t80) cc_final: 0.6495 (t80) REVERT: D 165 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7486 (mm-40) REVERT: D 168 ASP cc_start: 0.8224 (t0) cc_final: 0.7839 (t0) REVERT: D 201 ASP cc_start: 0.6923 (m-30) cc_final: 0.6715 (m-30) REVERT: E 34 GLU cc_start: 0.7399 (pt0) cc_final: 0.6980 (mm-30) REVERT: E 49 ASP cc_start: 0.8089 (p0) cc_final: 0.7856 (p0) REVERT: E 82 ARG cc_start: 0.7636 (ptt-90) cc_final: 0.6533 (ttt180) REVERT: E 96 MET cc_start: 0.8425 (mmm) cc_final: 0.8217 (mmm) REVERT: E 108 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7599 (mtmm) REVERT: E 118 MET cc_start: 0.7708 (tpt) cc_final: 0.7190 (tpt) REVERT: E 165 ASP cc_start: 0.7325 (m-30) cc_final: 0.7047 (m-30) REVERT: F 154 MET cc_start: 0.7545 (tmm) cc_final: 0.7310 (ttt) REVERT: F 157 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: F 170 GLU cc_start: 0.7702 (pp20) cc_final: 0.7497 (tm-30) REVERT: G 138 LYS cc_start: 0.8587 (ptmm) cc_final: 0.8291 (ptmm) REVERT: H 352 ILE cc_start: 0.9129 (mm) cc_final: 0.8860 (mt) REVERT: H 420 GLN cc_start: 0.8380 (mt0) cc_final: 0.7655 (mt0) REVERT: H 470 TYR cc_start: 0.7675 (t80) cc_final: 0.7469 (t80) REVERT: I 74 LEU cc_start: 0.8897 (pp) cc_final: 0.8525 (pp) REVERT: J 425 TRP cc_start: 0.6284 (t60) cc_final: 0.5937 (t-100) REVERT: J 432 MET cc_start: 0.8181 (mmp) cc_final: 0.7950 (mmm) REVERT: K 104 ASN cc_start: 0.6102 (p0) cc_final: 0.5107 (p0) REVERT: K 215 MET cc_start: 0.5903 (ppp) cc_final: 0.5048 (mmm) REVERT: L 73 ASP cc_start: 0.7700 (p0) cc_final: 0.7319 (p0) REVERT: L 169 GLU cc_start: 0.7755 (pp20) cc_final: 0.7441 (pp20) REVERT: L 173 GLU cc_start: 0.6524 (pt0) cc_final: 0.5789 (pt0) REVERT: M 414 GLU cc_start: 0.7367 (pp20) cc_final: 0.7046 (pm20) REVERT: M 420 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6653 (tt0) REVERT: M 456 ASP cc_start: 0.8584 (t0) cc_final: 0.8032 (t0) REVERT: M 476 GLU cc_start: 0.7816 (pm20) cc_final: 0.7421 (pm20) REVERT: N 64 ILE cc_start: 0.9051 (mm) cc_final: 0.8829 (mt) REVERT: N 122 LYS cc_start: 0.8011 (mttt) cc_final: 0.7684 (mtmt) REVERT: N 151 TRP cc_start: 0.8447 (t-100) cc_final: 0.8199 (t-100) REVERT: N 152 ARG cc_start: 0.7183 (mmt180) cc_final: 0.6938 (mmm-85) REVERT: N 291 ASN cc_start: 0.7953 (m-40) cc_final: 0.7736 (m110) REVERT: O 97 ASP cc_start: 0.7356 (t70) cc_final: 0.7009 (t0) REVERT: Q 51 GLN cc_start: 0.7290 (mm-40) cc_final: 0.6990 (mm-40) REVERT: Q 163 TYR cc_start: 0.2025 (t80) cc_final: 0.1456 (t80) REVERT: R 166 TYR cc_start: 0.5686 (p90) cc_final: 0.5341 (p90) REVERT: S 109 LEU cc_start: 0.4531 (OUTLIER) cc_final: 0.4282 (pp) REVERT: S 159 THR cc_start: 0.5126 (m) cc_final: 0.4713 (p) outliers start: 120 outliers final: 58 residues processed: 853 average time/residue: 0.3963 time to fit residues: 523.0415 Evaluate side-chains 696 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 629 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 460 ASP Chi-restraints excluded: chain J residue 494 TRP Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 19 ASP Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain M residue 406 CYS Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 247 ARG Chi-restraints excluded: chain N residue 331 ASP Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 190 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 128 GLU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 176 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 317 optimal weight: 0.4980 chunk 342 optimal weight: 8.9990 chunk 282 optimal weight: 0.7980 chunk 314 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN B 56 GLN B 75 ASN C 51 GLN ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 185 HIS D 141 GLN D 157 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN F 184 ASN ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 HIS ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 252 GLN ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28149 Z= 0.225 Angle : 0.644 13.752 38043 Z= 0.325 Chirality : 0.045 0.238 4287 Planarity : 0.004 0.046 4940 Dihedral : 4.619 46.069 3885 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.68 % Allowed : 21.59 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3543 helix: -1.27 (0.13), residues: 1396 sheet: -0.52 (0.23), residues: 517 loop : -1.81 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 425 HIS 0.011 0.001 HIS L 171 PHE 0.023 0.001 PHE S 174 TYR 0.024 0.001 TYR O 68 ARG 0.012 0.001 ARG S 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 713 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8878 (tppt) cc_final: 0.8524 (tptt) REVERT: A 174 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: A 176 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: B 71 ASP cc_start: 0.7459 (m-30) cc_final: 0.7188 (p0) REVERT: C 23 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7927 (mtm180) REVERT: C 127 SER cc_start: 0.8807 (t) cc_final: 0.8548 (p) REVERT: C 144 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7960 (mtmm) REVERT: C 164 GLU cc_start: 0.8614 (pt0) cc_final: 0.8052 (pp20) REVERT: C 171 TYR cc_start: 0.8133 (m-80) cc_final: 0.7882 (m-80) REVERT: D 83 TYR cc_start: 0.8346 (t80) cc_final: 0.7726 (t80) REVERT: D 96 TYR cc_start: 0.7974 (t80) cc_final: 0.7087 (t80) REVERT: D 128 LEU cc_start: 0.8736 (tp) cc_final: 0.8362 (tp) REVERT: D 157 GLN cc_start: 0.7942 (mt0) cc_final: 0.7687 (mt0) REVERT: D 165 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7556 (mm-40) REVERT: E 32 GLU cc_start: 0.7417 (tp30) cc_final: 0.6951 (tp30) REVERT: E 34 GLU cc_start: 0.7475 (pt0) cc_final: 0.7063 (mm-30) REVERT: E 49 ASP cc_start: 0.8015 (p0) cc_final: 0.7801 (p0) REVERT: E 82 ARG cc_start: 0.7576 (ptt-90) cc_final: 0.6470 (ttt180) REVERT: E 108 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7725 (mtmm) REVERT: E 111 SER cc_start: 0.6940 (t) cc_final: 0.6383 (t) REVERT: E 118 MET cc_start: 0.7877 (tpt) cc_final: 0.7476 (tpt) REVERT: F 89 ASN cc_start: 0.7652 (m-40) cc_final: 0.7247 (m-40) REVERT: F 154 MET cc_start: 0.7473 (tmm) cc_final: 0.7139 (ttt) REVERT: G 138 LYS cc_start: 0.8568 (ptmm) cc_final: 0.8302 (ptmm) REVERT: G 139 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8232 (tm-30) REVERT: H 378 THR cc_start: 0.9523 (t) cc_final: 0.9238 (m) REVERT: H 447 TYR cc_start: 0.8604 (m-80) cc_final: 0.7817 (m-80) REVERT: H 467 GLU cc_start: 0.6846 (pt0) cc_final: 0.6627 (pt0) REVERT: H 470 TYR cc_start: 0.7654 (t80) cc_final: 0.7400 (t80) REVERT: I 74 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8451 (pp) REVERT: I 88 SER cc_start: 0.8706 (t) cc_final: 0.8354 (m) REVERT: J 429 GLN cc_start: 0.7646 (mm110) cc_final: 0.6929 (mm110) REVERT: J 432 MET cc_start: 0.8210 (mmp) cc_final: 0.7707 (mmm) REVERT: K 47 GLN cc_start: 0.8460 (mt0) cc_final: 0.8129 (mt0) REVERT: K 104 ASN cc_start: 0.5870 (p0) cc_final: 0.5647 (p0) REVERT: K 215 MET cc_start: 0.5367 (ppp) cc_final: 0.4622 (mmm) REVERT: L 73 ASP cc_start: 0.7911 (p0) cc_final: 0.7457 (p0) REVERT: L 128 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8725 (pt) REVERT: L 169 GLU cc_start: 0.7602 (pp20) cc_final: 0.6577 (pp20) REVERT: L 173 GLU cc_start: 0.6392 (pt0) cc_final: 0.5451 (pt0) REVERT: L 179 ARG cc_start: 0.6948 (tpt170) cc_final: 0.6652 (tpt170) REVERT: M 420 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: M 456 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8167 (t0) REVERT: M 476 GLU cc_start: 0.7819 (pm20) cc_final: 0.7617 (pm20) REVERT: N 19 ASP cc_start: 0.7986 (p0) cc_final: 0.7448 (p0) REVERT: N 42 GLU cc_start: 0.5562 (mm-30) cc_final: 0.5349 (mm-30) REVERT: N 47 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7654 (mm-30) REVERT: N 106 VAL cc_start: 0.8156 (t) cc_final: 0.7905 (t) REVERT: N 152 ARG cc_start: 0.7147 (mmt180) cc_final: 0.6765 (mmm-85) REVERT: Q 51 GLN cc_start: 0.7148 (mm-40) cc_final: 0.6875 (mm-40) REVERT: Q 81 MET cc_start: 0.6798 (ppp) cc_final: 0.6472 (ppp) REVERT: Q 163 TYR cc_start: 0.2327 (t80) cc_final: 0.1531 (t80) REVERT: R 8 PHE cc_start: 0.5162 (OUTLIER) cc_final: 0.4649 (m-80) REVERT: R 39 VAL cc_start: -0.1805 (OUTLIER) cc_final: -0.2124 (m) REVERT: R 165 MET cc_start: 0.6670 (tpp) cc_final: 0.6385 (tpp) REVERT: R 166 TYR cc_start: 0.5723 (p90) cc_final: 0.5365 (p90) REVERT: S 19 LEU cc_start: 0.5143 (tp) cc_final: 0.4832 (tp) REVERT: S 109 LEU cc_start: 0.4842 (OUTLIER) cc_final: 0.4552 (pp) REVERT: S 159 THR cc_start: 0.5170 (m) cc_final: 0.4768 (p) outliers start: 109 outliers final: 67 residues processed: 785 average time/residue: 0.4017 time to fit residues: 489.9760 Evaluate side-chains 722 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 645 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 373 LYS Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 364 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain M residue 406 CYS Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain M residue 456 ASP Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 PHE Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 247 ARG Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain Q residue 3 ILE Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 8 PHE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 313 optimal weight: 0.6980 chunk 238 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 213 optimal weight: 0.7980 chunk 318 optimal weight: 0.9980 chunk 337 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 301 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN B 75 ASN ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 HIS ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS L 98 ASN ** L 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28149 Z= 0.171 Angle : 0.602 13.683 38043 Z= 0.298 Chirality : 0.044 0.184 4287 Planarity : 0.004 0.068 4940 Dihedral : 4.421 42.786 3885 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.72 % Allowed : 22.47 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 3543 helix: -0.60 (0.13), residues: 1391 sheet: -0.42 (0.22), residues: 533 loop : -1.63 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 208 HIS 0.004 0.001 HIS C 120 PHE 0.029 0.001 PHE N 92 TYR 0.019 0.001 TYR O 68 ARG 0.015 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 693 time to evaluate : 3.163 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: A 51 LYS cc_start: 0.8868 (tppt) cc_final: 0.8514 (tptt) REVERT: A 176 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: C 23 ARG cc_start: 0.8269 (mtm110) cc_final: 0.7956 (mtm180) REVERT: C 51 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: C 127 SER cc_start: 0.8775 (t) cc_final: 0.8511 (p) REVERT: C 141 MET cc_start: 0.8767 (mmp) cc_final: 0.8148 (mmm) REVERT: C 144 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7712 (mtmm) REVERT: C 164 GLU cc_start: 0.8608 (pt0) cc_final: 0.7997 (pp20) REVERT: D 83 TYR cc_start: 0.8384 (t80) cc_final: 0.7711 (t80) REVERT: D 96 TYR cc_start: 0.8076 (t80) cc_final: 0.6735 (t80) REVERT: D 128 LEU cc_start: 0.8749 (tp) cc_final: 0.8393 (tp) REVERT: D 157 GLN cc_start: 0.7798 (mt0) cc_final: 0.7259 (mt0) REVERT: D 165 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7477 (mm-40) REVERT: D 180 LYS cc_start: 0.8512 (ttmt) cc_final: 0.7659 (ttmt) REVERT: E 32 GLU cc_start: 0.7350 (tp30) cc_final: 0.6913 (tp30) REVERT: E 34 GLU cc_start: 0.7465 (pt0) cc_final: 0.7051 (mm-30) REVERT: E 49 ASP cc_start: 0.8027 (p0) cc_final: 0.7799 (p0) REVERT: E 82 ARG cc_start: 0.7497 (ptt-90) cc_final: 0.6558 (ttt180) REVERT: E 108 LYS cc_start: 0.8183 (ptpt) cc_final: 0.7658 (mtmm) REVERT: E 111 SER cc_start: 0.6903 (t) cc_final: 0.6362 (t) REVERT: E 118 MET cc_start: 0.7603 (tpt) cc_final: 0.7354 (tpt) REVERT: F 89 ASN cc_start: 0.7715 (m-40) cc_final: 0.7499 (m-40) REVERT: F 154 MET cc_start: 0.7534 (tmm) cc_final: 0.7067 (ttt) REVERT: G 138 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8347 (ptmm) REVERT: G 141 MET cc_start: 0.8562 (mtp) cc_final: 0.8271 (mtt) REVERT: H 378 THR cc_start: 0.9457 (t) cc_final: 0.9195 (m) REVERT: H 420 GLN cc_start: 0.8345 (mt0) cc_final: 0.7668 (mt0) REVERT: H 447 TYR cc_start: 0.8592 (m-80) cc_final: 0.7805 (m-80) REVERT: I 74 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8452 (pp) REVERT: J 425 TRP cc_start: 0.5914 (t-100) cc_final: 0.5628 (t-100) REVERT: K 49 PHE cc_start: 0.8430 (m-10) cc_final: 0.8207 (m-10) REVERT: K 104 ASN cc_start: 0.6129 (p0) cc_final: 0.5904 (p0) REVERT: K 215 MET cc_start: 0.5418 (ppp) cc_final: 0.4659 (mmm) REVERT: L 79 ILE cc_start: 0.9098 (pt) cc_final: 0.8830 (mt) REVERT: L 98 ASN cc_start: 0.8174 (m-40) cc_final: 0.7596 (t0) REVERT: L 169 GLU cc_start: 0.7517 (pp20) cc_final: 0.6676 (pp20) REVERT: L 173 GLU cc_start: 0.6335 (pt0) cc_final: 0.5626 (pt0) REVERT: L 179 ARG cc_start: 0.7010 (tpt170) cc_final: 0.6755 (tpt170) REVERT: L 212 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8332 (mmmt) REVERT: M 420 GLN cc_start: 0.7218 (tm-30) cc_final: 0.6824 (tt0) REVERT: M 456 ASP cc_start: 0.8722 (t0) cc_final: 0.8268 (t0) REVERT: M 466 MET cc_start: 0.7856 (tpp) cc_final: 0.7654 (ttt) REVERT: N 19 ASP cc_start: 0.7944 (p0) cc_final: 0.7432 (p0) REVERT: N 106 VAL cc_start: 0.8119 (t) cc_final: 0.7904 (t) REVERT: N 152 ARG cc_start: 0.7116 (mmt180) cc_final: 0.6898 (mmm-85) REVERT: N 180 MET cc_start: 0.8159 (ttm) cc_final: 0.7869 (ttm) REVERT: P 72 MET cc_start: 0.5240 (tmm) cc_final: 0.4994 (tmm) REVERT: Q 1 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5720 (pp20) REVERT: Q 35 LEU cc_start: 0.7770 (mt) cc_final: 0.7164 (mp) REVERT: Q 51 GLN cc_start: 0.7181 (mm-40) cc_final: 0.6966 (mm-40) REVERT: Q 81 MET cc_start: 0.6970 (ppp) cc_final: 0.6726 (ppp) REVERT: Q 163 TYR cc_start: 0.2180 (t80) cc_final: 0.1419 (t80) REVERT: R 8 PHE cc_start: 0.5053 (OUTLIER) cc_final: 0.4569 (m-80) REVERT: R 39 VAL cc_start: -0.1922 (OUTLIER) cc_final: -0.2246 (m) REVERT: R 165 MET cc_start: 0.6455 (tpp) cc_final: 0.6196 (tpp) REVERT: R 166 TYR cc_start: 0.5741 (p90) cc_final: 0.5277 (p90) REVERT: S 19 LEU cc_start: 0.5175 (tp) cc_final: 0.4870 (tp) REVERT: S 109 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4479 (pp) REVERT: S 159 THR cc_start: 0.5055 (m) cc_final: 0.4672 (p) outliers start: 110 outliers final: 70 residues processed: 764 average time/residue: 0.3935 time to fit residues: 470.8122 Evaluate side-chains 713 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 635 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 165 TYR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 373 LYS Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 364 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 186 ASN Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 422 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 313 TYR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain Q residue 1 GLU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain R residue 8 PHE Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 280 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 287 optimal weight: 8.9990 chunk 233 optimal weight: 0.0020 chunk 0 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 302 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN B 75 ASN C 44 GLN C 51 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN J 366 HIS ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 ASN ** L 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 28149 Z= 0.286 Angle : 0.682 14.495 38043 Z= 0.343 Chirality : 0.046 0.393 4287 Planarity : 0.004 0.063 4940 Dihedral : 4.810 50.419 3885 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.80 % Allowed : 23.14 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3543 helix: -0.37 (0.14), residues: 1437 sheet: -0.39 (0.23), residues: 531 loop : -1.59 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 425 HIS 0.022 0.002 HIS K 5 PHE 0.024 0.002 PHE F 135 TYR 0.018 0.002 TYR J 462 ARG 0.011 0.001 ARG G 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 669 time to evaluate : 3.180 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: A 51 LYS cc_start: 0.8881 (tppt) cc_final: 0.8538 (tptt) REVERT: A 176 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: B 56 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7646 (mm-40) REVERT: B 104 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8983 (t) REVERT: C 23 ARG cc_start: 0.8281 (mtm110) cc_final: 0.7953 (mtm180) REVERT: C 32 GLU cc_start: 0.6922 (tm-30) cc_final: 0.5969 (tm-30) REVERT: C 34 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7480 (mp0) REVERT: C 90 PHE cc_start: 0.8473 (m-80) cc_final: 0.8227 (m-80) REVERT: C 134 GLU cc_start: 0.7545 (tp30) cc_final: 0.7153 (tp30) REVERT: C 144 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7692 (mtmm) REVERT: C 164 GLU cc_start: 0.8649 (pt0) cc_final: 0.8047 (pp20) REVERT: D 83 TYR cc_start: 0.8607 (t80) cc_final: 0.7970 (t80) REVERT: D 96 TYR cc_start: 0.7662 (t80) cc_final: 0.6974 (t80) REVERT: D 114 MET cc_start: 0.8253 (mtp) cc_final: 0.8008 (mtp) REVERT: D 128 LEU cc_start: 0.8782 (tp) cc_final: 0.8433 (tp) REVERT: D 157 GLN cc_start: 0.7964 (mt0) cc_final: 0.7529 (mt0) REVERT: D 165 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7478 (mm-40) REVERT: D 175 GLU cc_start: 0.8389 (tp30) cc_final: 0.8051 (tp30) REVERT: D 180 LYS cc_start: 0.8644 (ttmt) cc_final: 0.7947 (ttmt) REVERT: E 34 GLU cc_start: 0.7374 (pt0) cc_final: 0.6975 (mm-30) REVERT: E 49 ASP cc_start: 0.8134 (p0) cc_final: 0.7901 (p0) REVERT: E 82 ARG cc_start: 0.7520 (ptt-90) cc_final: 0.6558 (ttt180) REVERT: E 100 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9205 (mt) REVERT: E 108 LYS cc_start: 0.8511 (ptpt) cc_final: 0.8031 (mtmm) REVERT: E 111 SER cc_start: 0.7900 (t) cc_final: 0.7525 (t) REVERT: E 118 MET cc_start: 0.7771 (tpt) cc_final: 0.7317 (tpt) REVERT: E 134 GLU cc_start: 0.7979 (pp20) cc_final: 0.7659 (pp20) REVERT: E 176 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6842 (tm-30) REVERT: F 153 ILE cc_start: 0.9101 (mm) cc_final: 0.8894 (mm) REVERT: F 154 MET cc_start: 0.7936 (tmm) cc_final: 0.7542 (ttt) REVERT: H 378 THR cc_start: 0.9549 (t) cc_final: 0.9227 (m) REVERT: H 447 TYR cc_start: 0.8669 (m-80) cc_final: 0.7845 (m-80) REVERT: I 74 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8501 (pp) REVERT: I 88 SER cc_start: 0.8800 (t) cc_final: 0.8411 (m) REVERT: I 146 MET cc_start: 0.7783 (mmm) cc_final: 0.7569 (mmm) REVERT: J 408 THR cc_start: 0.8602 (m) cc_final: 0.8318 (p) REVERT: J 425 TRP cc_start: 0.6241 (t-100) cc_final: 0.5850 (t-100) REVERT: J 429 GLN cc_start: 0.7865 (mm110) cc_final: 0.7601 (mm-40) REVERT: K 47 GLN cc_start: 0.8282 (mt0) cc_final: 0.7764 (mt0) REVERT: K 49 PHE cc_start: 0.8363 (m-10) cc_final: 0.8138 (m-10) REVERT: K 104 ASN cc_start: 0.6177 (p0) cc_final: 0.4385 (p0) REVERT: K 106 PHE cc_start: 0.7107 (m-10) cc_final: 0.6595 (m-10) REVERT: K 215 MET cc_start: 0.5540 (ppp) cc_final: 0.4885 (mmm) REVERT: L 79 ILE cc_start: 0.9153 (pt) cc_final: 0.8948 (mt) REVERT: L 98 ASN cc_start: 0.8420 (m110) cc_final: 0.7893 (t0) REVERT: L 169 GLU cc_start: 0.7727 (pp20) cc_final: 0.6666 (pp20) REVERT: L 173 GLU cc_start: 0.6517 (pt0) cc_final: 0.5551 (pt0) REVERT: L 179 ARG cc_start: 0.7047 (tpt170) cc_final: 0.6753 (tpt170) REVERT: L 212 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8770 (mmmm) REVERT: M 420 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: M 456 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8309 (t0) REVERT: M 476 GLU cc_start: 0.8054 (pm20) cc_final: 0.7799 (pm20) REVERT: N 19 ASP cc_start: 0.8005 (p0) cc_final: 0.7488 (p0) REVERT: N 47 GLU cc_start: 0.8423 (tp30) cc_final: 0.8085 (tp30) REVERT: N 146 GLU cc_start: 0.7213 (pp20) cc_final: 0.6838 (pp20) REVERT: N 152 ARG cc_start: 0.7231 (mmt180) cc_final: 0.6961 (mmm-85) REVERT: N 180 MET cc_start: 0.8325 (ttm) cc_final: 0.8061 (ttm) REVERT: N 250 MET cc_start: 0.7565 (tmm) cc_final: 0.7328 (tmm) REVERT: P 72 MET cc_start: 0.5148 (tmm) cc_final: 0.4877 (tmm) REVERT: P 99 MET cc_start: 0.5248 (mmp) cc_final: 0.4518 (mpp) REVERT: Q 51 GLN cc_start: 0.7307 (mm-40) cc_final: 0.7058 (mm-40) REVERT: Q 81 MET cc_start: 0.6812 (ppp) cc_final: 0.6589 (ppp) REVERT: Q 163 TYR cc_start: 0.2311 (t80) cc_final: 0.1569 (t80) REVERT: R 39 VAL cc_start: -0.1387 (OUTLIER) cc_final: -0.1764 (m) REVERT: R 165 MET cc_start: 0.6490 (tpp) cc_final: 0.6091 (tpp) REVERT: S 19 LEU cc_start: 0.5288 (tp) cc_final: 0.4972 (tp) REVERT: S 159 THR cc_start: 0.5259 (m) cc_final: 0.4785 (p) REVERT: S 180 ASN cc_start: 0.6234 (OUTLIER) cc_final: 0.5797 (p0) outliers start: 142 outliers final: 98 residues processed: 754 average time/residue: 0.3961 time to fit residues: 465.3563 Evaluate side-chains 726 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 619 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 364 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 423 ASP Chi-restraints excluded: chain J residue 479 THR Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 186 ASN Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain M residue 433 LYS Chi-restraints excluded: chain M residue 456 ASP Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 247 ARG Chi-restraints excluded: chain N residue 331 ASP Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 139 ASP Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 172 THR Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 180 ASN Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 113 optimal weight: 0.6980 chunk 303 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 337 optimal weight: 0.0570 chunk 280 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 75 ASN C 24 GLN C 44 GLN C 51 GLN ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 HIS ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 ASN L 157 HIS ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28149 Z= 0.173 Angle : 0.624 13.783 38043 Z= 0.305 Chirality : 0.044 0.288 4287 Planarity : 0.004 0.045 4940 Dihedral : 4.567 48.285 3885 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.75 % Allowed : 25.10 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3543 helix: -0.09 (0.14), residues: 1433 sheet: -0.37 (0.23), residues: 519 loop : -1.49 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 208 HIS 0.007 0.001 HIS K 5 PHE 0.032 0.001 PHE N 92 TYR 0.015 0.001 TYR O 68 ARG 0.005 0.000 ARG R 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 681 time to evaluate : 3.278 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: A 51 LYS cc_start: 0.8782 (tppt) cc_final: 0.8498 (tptt) REVERT: A 141 SER cc_start: 0.7685 (p) cc_final: 0.7340 (p) REVERT: A 176 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: B 50 PHE cc_start: 0.8942 (t80) cc_final: 0.8707 (t80) REVERT: B 154 MET cc_start: 0.7690 (tmm) cc_final: 0.7438 (tmm) REVERT: C 23 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7920 (mtm180) REVERT: C 32 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6056 (tm-30) REVERT: C 34 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7104 (mp0) REVERT: C 51 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8574 (mt0) REVERT: C 129 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7967 (mm-40) REVERT: C 134 GLU cc_start: 0.7566 (tp30) cc_final: 0.7224 (tp30) REVERT: C 144 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7651 (mtmm) REVERT: C 164 GLU cc_start: 0.8632 (pt0) cc_final: 0.7981 (pp20) REVERT: D 83 TYR cc_start: 0.8536 (t80) cc_final: 0.8177 (t80) REVERT: D 96 TYR cc_start: 0.7589 (t80) cc_final: 0.6585 (t80) REVERT: D 114 MET cc_start: 0.8186 (mtp) cc_final: 0.7899 (mtp) REVERT: D 128 LEU cc_start: 0.8809 (tp) cc_final: 0.8467 (tp) REVERT: D 157 GLN cc_start: 0.7911 (mt0) cc_final: 0.7333 (mt0) REVERT: D 165 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7554 (mt0) REVERT: D 180 LYS cc_start: 0.8652 (ttmt) cc_final: 0.7776 (ttmt) REVERT: E 34 GLU cc_start: 0.7649 (pt0) cc_final: 0.7200 (mm-30) REVERT: E 96 MET cc_start: 0.8186 (mmp) cc_final: 0.7889 (mmm) REVERT: E 100 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9168 (mt) REVERT: E 108 LYS cc_start: 0.8372 (ptpt) cc_final: 0.7857 (mtmm) REVERT: E 111 SER cc_start: 0.7733 (t) cc_final: 0.7321 (t) REVERT: E 118 MET cc_start: 0.7689 (tpt) cc_final: 0.7277 (tpt) REVERT: E 135 ILE cc_start: 0.8984 (tp) cc_final: 0.8769 (pt) REVERT: G 139 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8301 (tm-30) REVERT: G 141 MET cc_start: 0.8588 (mtp) cc_final: 0.8311 (mtt) REVERT: H 378 THR cc_start: 0.9511 (t) cc_final: 0.9227 (m) REVERT: H 420 GLN cc_start: 0.8517 (mt0) cc_final: 0.7894 (mt0) REVERT: H 447 TYR cc_start: 0.8508 (m-80) cc_final: 0.7470 (m-80) REVERT: I 74 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8465 (pp) REVERT: I 88 SER cc_start: 0.8875 (t) cc_final: 0.8478 (m) REVERT: J 408 THR cc_start: 0.8601 (m) cc_final: 0.8331 (p) REVERT: J 425 TRP cc_start: 0.6020 (t-100) cc_final: 0.5692 (t-100) REVERT: J 429 GLN cc_start: 0.7838 (mm110) cc_final: 0.7611 (mm-40) REVERT: J 438 VAL cc_start: 0.9100 (m) cc_final: 0.8882 (p) REVERT: K 34 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7004 (mpp) REVERT: K 104 ASN cc_start: 0.6332 (p0) cc_final: 0.6009 (p0) REVERT: K 215 MET cc_start: 0.5526 (ppp) cc_final: 0.4895 (mmm) REVERT: L 54 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8247 (tp) REVERT: L 79 ILE cc_start: 0.9126 (pt) cc_final: 0.8867 (mt) REVERT: L 98 ASN cc_start: 0.8144 (m-40) cc_final: 0.7665 (t0) REVERT: L 169 GLU cc_start: 0.7633 (pp20) cc_final: 0.6555 (pp20) REVERT: L 172 ILE cc_start: 0.8739 (mt) cc_final: 0.8388 (tp) REVERT: L 173 GLU cc_start: 0.6487 (pt0) cc_final: 0.5827 (pt0) REVERT: L 179 ARG cc_start: 0.7249 (tpt170) cc_final: 0.7016 (tpt170) REVERT: M 420 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6796 (tt0) REVERT: M 456 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8577 (t0) REVERT: N 19 ASP cc_start: 0.7919 (p0) cc_final: 0.7462 (p0) REVERT: N 47 GLU cc_start: 0.8422 (tp30) cc_final: 0.8095 (tp30) REVERT: N 143 GLN cc_start: 0.8097 (tt0) cc_final: 0.7768 (tt0) REVERT: N 152 ARG cc_start: 0.7075 (mmt180) cc_final: 0.6770 (mmm-85) REVERT: N 180 MET cc_start: 0.8194 (ttm) cc_final: 0.7933 (ttm) REVERT: N 244 ASP cc_start: 0.7119 (p0) cc_final: 0.6378 (p0) REVERT: N 250 MET cc_start: 0.7464 (tmm) cc_final: 0.7139 (tmm) REVERT: P 72 MET cc_start: 0.5001 (tmm) cc_final: 0.4722 (tmm) REVERT: P 93 VAL cc_start: 0.7201 (OUTLIER) cc_final: 0.6935 (t) REVERT: P 99 MET cc_start: 0.4544 (mmp) cc_final: 0.4279 (mpp) REVERT: Q 1 GLU cc_start: 0.5577 (OUTLIER) cc_final: 0.5342 (pp20) REVERT: Q 81 MET cc_start: 0.6748 (ppp) cc_final: 0.6543 (ppp) REVERT: Q 163 TYR cc_start: 0.2006 (t80) cc_final: 0.1286 (t80) REVERT: R 39 VAL cc_start: -0.1687 (OUTLIER) cc_final: -0.2067 (m) REVERT: R 165 MET cc_start: 0.6411 (tpp) cc_final: 0.6062 (tpp) REVERT: S 19 LEU cc_start: 0.5271 (tp) cc_final: 0.4932 (tp) REVERT: S 114 LYS cc_start: 0.4697 (mmtm) cc_final: 0.4422 (pttp) REVERT: S 135 PHE cc_start: 0.7297 (m-10) cc_final: 0.6934 (m-10) REVERT: S 159 THR cc_start: 0.5146 (m) cc_final: 0.4700 (p) outliers start: 111 outliers final: 69 residues processed: 749 average time/residue: 0.3877 time to fit residues: 453.8102 Evaluate side-chains 716 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 635 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain J residue 364 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 479 THR Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 186 ASN Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 364 THR Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain M residue 433 LYS Chi-restraints excluded: chain M residue 456 ASP Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain Q residue 1 GLU Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 325 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 192 optimal weight: 0.2980 chunk 246 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 336 optimal weight: 0.0970 chunk 210 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN B 75 ASN C 51 GLN ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN E 44 GLN E 121 GLN ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 ASN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN ** Q 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28149 Z= 0.171 Angle : 0.622 15.016 38043 Z= 0.304 Chirality : 0.044 0.230 4287 Planarity : 0.004 0.048 4940 Dihedral : 4.457 47.366 3885 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.14 % Allowed : 26.11 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3543 helix: 0.13 (0.14), residues: 1417 sheet: -0.32 (0.23), residues: 523 loop : -1.44 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 208 HIS 0.005 0.001 HIS M 366 PHE 0.026 0.001 PHE F 135 TYR 0.020 0.001 TYR N 185 ARG 0.007 0.000 ARG M 435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 647 time to evaluate : 3.063 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: A 50 ASP cc_start: 0.8073 (p0) cc_final: 0.7854 (p0) REVERT: A 51 LYS cc_start: 0.8757 (tppt) cc_final: 0.8441 (tptt) REVERT: A 141 SER cc_start: 0.7614 (p) cc_final: 0.7397 (p) REVERT: A 174 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: A 176 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: A 203 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7281 (mtt90) REVERT: B 50 PHE cc_start: 0.8950 (t80) cc_final: 0.8719 (t80) REVERT: B 118 ARG cc_start: 0.8567 (mtt90) cc_final: 0.8364 (mpp80) REVERT: B 154 MET cc_start: 0.7702 (tmm) cc_final: 0.7427 (tmm) REVERT: C 23 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7885 (mtm180) REVERT: C 32 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6175 (tm-30) REVERT: C 34 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7116 (mp0) REVERT: C 51 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: C 134 GLU cc_start: 0.7554 (tp30) cc_final: 0.7188 (tp30) REVERT: C 142 TYR cc_start: 0.8522 (t80) cc_final: 0.8231 (t80) REVERT: C 164 GLU cc_start: 0.8631 (pt0) cc_final: 0.7975 (pp20) REVERT: D 83 TYR cc_start: 0.8480 (t80) cc_final: 0.8154 (t80) REVERT: D 96 TYR cc_start: 0.7541 (t80) cc_final: 0.6498 (t80) REVERT: D 114 MET cc_start: 0.8178 (mtp) cc_final: 0.7899 (mtp) REVERT: D 128 LEU cc_start: 0.8750 (tp) cc_final: 0.8434 (tp) REVERT: D 135 PHE cc_start: 0.8420 (t80) cc_final: 0.8169 (t80) REVERT: D 157 GLN cc_start: 0.7910 (mt0) cc_final: 0.7288 (mt0) REVERT: D 165 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7533 (mt0) REVERT: D 180 LYS cc_start: 0.8661 (ttmt) cc_final: 0.7762 (ttmt) REVERT: D 216 TYR cc_start: 0.8299 (t80) cc_final: 0.7797 (t80) REVERT: E 34 GLU cc_start: 0.7220 (pt0) cc_final: 0.6972 (mm-30) REVERT: E 100 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9210 (mt) REVERT: E 108 LYS cc_start: 0.8366 (ptpt) cc_final: 0.7835 (mtmm) REVERT: E 111 SER cc_start: 0.7687 (t) cc_final: 0.7276 (t) REVERT: E 118 MET cc_start: 0.7661 (tpt) cc_final: 0.7257 (tpt) REVERT: E 135 ILE cc_start: 0.8972 (tp) cc_final: 0.8725 (pt) REVERT: F 154 MET cc_start: 0.7868 (tmm) cc_final: 0.7250 (ttt) REVERT: G 139 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8263 (tm-30) REVERT: H 350 MET cc_start: 0.4899 (tpt) cc_final: 0.4536 (tpt) REVERT: H 378 THR cc_start: 0.9489 (t) cc_final: 0.9238 (m) REVERT: H 420 GLN cc_start: 0.8461 (mt0) cc_final: 0.7839 (mt0) REVERT: H 446 THR cc_start: 0.9265 (p) cc_final: 0.9033 (t) REVERT: H 447 TYR cc_start: 0.8426 (m-80) cc_final: 0.7624 (m-80) REVERT: I 74 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8479 (pp) REVERT: I 88 SER cc_start: 0.8865 (t) cc_final: 0.8431 (m) REVERT: J 408 THR cc_start: 0.8584 (m) cc_final: 0.8294 (p) REVERT: J 425 TRP cc_start: 0.5982 (t-100) cc_final: 0.5527 (t-100) REVERT: J 429 GLN cc_start: 0.7952 (mm110) cc_final: 0.7420 (mm110) REVERT: J 438 VAL cc_start: 0.9133 (m) cc_final: 0.8875 (p) REVERT: K 34 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6921 (mpp) REVERT: K 104 ASN cc_start: 0.6717 (p0) cc_final: 0.6421 (p0) REVERT: K 215 MET cc_start: 0.5547 (ppp) cc_final: 0.4899 (mmm) REVERT: L 54 LEU cc_start: 0.8741 (tt) cc_final: 0.8498 (tp) REVERT: L 79 ILE cc_start: 0.9118 (pt) cc_final: 0.8878 (mt) REVERT: L 98 ASN cc_start: 0.8287 (m110) cc_final: 0.7739 (t0) REVERT: L 169 GLU cc_start: 0.7526 (pp20) cc_final: 0.6468 (pp20) REVERT: L 172 ILE cc_start: 0.8746 (mt) cc_final: 0.8351 (tp) REVERT: L 173 GLU cc_start: 0.6499 (pt0) cc_final: 0.5719 (pt0) REVERT: L 179 ARG cc_start: 0.7271 (tpt170) cc_final: 0.6821 (tpt170) REVERT: M 420 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: M 456 ASP cc_start: 0.8847 (t0) cc_final: 0.8551 (t0) REVERT: N 19 ASP cc_start: 0.7896 (p0) cc_final: 0.7452 (p0) REVERT: N 47 GLU cc_start: 0.8452 (tp30) cc_final: 0.8147 (tp30) REVERT: N 152 ARG cc_start: 0.7053 (mmt180) cc_final: 0.6739 (mmm-85) REVERT: N 180 MET cc_start: 0.8113 (ttm) cc_final: 0.7771 (ttm) REVERT: N 244 ASP cc_start: 0.7122 (p0) cc_final: 0.6384 (p0) REVERT: N 250 MET cc_start: 0.7568 (tmm) cc_final: 0.7214 (tmm) REVERT: P 16 MET cc_start: 0.6669 (tpt) cc_final: 0.6458 (tpt) REVERT: P 72 MET cc_start: 0.5229 (tmm) cc_final: 0.4563 (tmm) REVERT: Q 163 TYR cc_start: 0.1934 (t80) cc_final: 0.1231 (t80) REVERT: R 39 VAL cc_start: -0.1715 (OUTLIER) cc_final: -0.2116 (m) REVERT: R 165 MET cc_start: 0.6249 (tpp) cc_final: 0.5953 (tpp) REVERT: S 19 LEU cc_start: 0.5249 (tp) cc_final: 0.4906 (tp) REVERT: S 159 THR cc_start: 0.5145 (m) cc_final: 0.4757 (p) outliers start: 93 outliers final: 68 residues processed: 706 average time/residue: 0.3981 time to fit residues: 440.9310 Evaluate side-chains 697 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 621 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain J residue 364 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 479 THR Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain M residue 433 LYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 98 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 208 optimal weight: 0.7980 chunk 134 optimal weight: 0.0870 chunk 200 optimal weight: 0.0970 chunk 101 optimal weight: 0.0000 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 chunk 213 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 264 optimal weight: 0.0470 overall best weight: 0.0658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 75 ASN C 51 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 HIS ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN Q 71 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28149 Z= 0.160 Angle : 0.636 13.577 38043 Z= 0.305 Chirality : 0.044 0.202 4287 Planarity : 0.004 0.052 4940 Dihedral : 4.322 44.400 3885 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.01 % Allowed : 26.39 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3543 helix: 0.22 (0.14), residues: 1415 sheet: -0.36 (0.23), residues: 520 loop : -1.36 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 208 HIS 0.004 0.001 HIS M 366 PHE 0.038 0.001 PHE N 92 TYR 0.028 0.001 TYR N 185 ARG 0.008 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 673 time to evaluate : 3.326 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: A 50 ASP cc_start: 0.8096 (p0) cc_final: 0.7887 (p0) REVERT: A 51 LYS cc_start: 0.8765 (tppt) cc_final: 0.8469 (tptt) REVERT: A 134 MET cc_start: 0.8344 (mtp) cc_final: 0.8139 (ptp) REVERT: A 141 SER cc_start: 0.7685 (p) cc_final: 0.7385 (p) REVERT: A 176 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: B 50 PHE cc_start: 0.8924 (t80) cc_final: 0.8653 (t80) REVERT: B 118 ARG cc_start: 0.8528 (mtt90) cc_final: 0.7971 (mpt-90) REVERT: C 23 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7880 (mtm180) REVERT: C 32 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6148 (tm-30) REVERT: C 34 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7092 (mp0) REVERT: C 51 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: C 92 LEU cc_start: 0.8616 (tp) cc_final: 0.8356 (tt) REVERT: C 134 GLU cc_start: 0.7488 (tp30) cc_final: 0.7107 (tp30) REVERT: C 142 TYR cc_start: 0.8540 (t80) cc_final: 0.8316 (t80) REVERT: C 164 GLU cc_start: 0.8620 (pt0) cc_final: 0.7977 (pp20) REVERT: D 83 TYR cc_start: 0.8478 (t80) cc_final: 0.8203 (t80) REVERT: D 96 TYR cc_start: 0.7490 (t80) cc_final: 0.6724 (t80) REVERT: D 128 LEU cc_start: 0.8768 (tp) cc_final: 0.8506 (tp) REVERT: D 135 PHE cc_start: 0.8394 (t80) cc_final: 0.8169 (t80) REVERT: D 157 GLN cc_start: 0.7936 (mt0) cc_final: 0.7325 (mt0) REVERT: D 165 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7568 (mt0) REVERT: D 180 LYS cc_start: 0.8665 (ttmt) cc_final: 0.7703 (ttmt) REVERT: D 184 ASN cc_start: 0.8829 (m-40) cc_final: 0.8595 (m-40) REVERT: D 216 TYR cc_start: 0.8204 (t80) cc_final: 0.7758 (t80) REVERT: D 222 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7871 (tp) REVERT: E 32 GLU cc_start: 0.7100 (tp30) cc_final: 0.6769 (tp30) REVERT: E 34 GLU cc_start: 0.7436 (pt0) cc_final: 0.7101 (mm-30) REVERT: E 82 ARG cc_start: 0.7356 (ptt-90) cc_final: 0.6555 (ttt180) REVERT: E 100 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9203 (mt) REVERT: E 108 LYS cc_start: 0.8277 (ptpt) cc_final: 0.7672 (mtmm) REVERT: E 111 SER cc_start: 0.7529 (t) cc_final: 0.7073 (t) REVERT: E 118 MET cc_start: 0.7457 (tpt) cc_final: 0.7103 (tpt) REVERT: F 154 MET cc_start: 0.7877 (tmm) cc_final: 0.7217 (ttt) REVERT: G 139 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8239 (tm-30) REVERT: G 141 MET cc_start: 0.8584 (mtp) cc_final: 0.8194 (mtt) REVERT: H 350 MET cc_start: 0.4820 (tpt) cc_final: 0.4460 (tpt) REVERT: H 378 THR cc_start: 0.9450 (t) cc_final: 0.9227 (m) REVERT: H 420 GLN cc_start: 0.8478 (mt0) cc_final: 0.7790 (mt0) REVERT: H 446 THR cc_start: 0.9307 (p) cc_final: 0.9105 (t) REVERT: H 447 TYR cc_start: 0.8414 (m-80) cc_final: 0.7677 (m-80) REVERT: I 74 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8499 (pp) REVERT: I 146 MET cc_start: 0.7857 (mmm) cc_final: 0.7355 (mmm) REVERT: J 408 THR cc_start: 0.8500 (m) cc_final: 0.8180 (p) REVERT: J 438 VAL cc_start: 0.9125 (m) cc_final: 0.8876 (p) REVERT: K 215 MET cc_start: 0.5513 (ppp) cc_final: 0.4852 (mmm) REVERT: L 79 ILE cc_start: 0.9047 (pt) cc_final: 0.8836 (mt) REVERT: L 98 ASN cc_start: 0.8036 (m110) cc_final: 0.7654 (t0) REVERT: L 169 GLU cc_start: 0.7570 (pp20) cc_final: 0.6582 (pp20) REVERT: L 172 ILE cc_start: 0.8707 (mt) cc_final: 0.8282 (tp) REVERT: L 173 GLU cc_start: 0.6533 (pt0) cc_final: 0.5751 (pt0) REVERT: L 179 ARG cc_start: 0.7229 (tpt170) cc_final: 0.6804 (tpt170) REVERT: M 420 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6778 (tt0) REVERT: M 456 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8525 (t0) REVERT: N 19 ASP cc_start: 0.7872 (p0) cc_final: 0.7515 (p0) REVERT: N 47 GLU cc_start: 0.8402 (tp30) cc_final: 0.8083 (tp30) REVERT: N 106 VAL cc_start: 0.8092 (t) cc_final: 0.7881 (t) REVERT: N 152 ARG cc_start: 0.7022 (mmt180) cc_final: 0.6648 (mmm-85) REVERT: N 180 MET cc_start: 0.7912 (ttm) cc_final: 0.7587 (ttm) REVERT: N 192 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8969 (mm) REVERT: N 199 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: N 244 ASP cc_start: 0.7094 (p0) cc_final: 0.6364 (p0) REVERT: N 250 MET cc_start: 0.7602 (tmm) cc_final: 0.7235 (tmm) REVERT: O 93 ILE cc_start: 0.8664 (mp) cc_final: 0.8283 (mt) REVERT: P 16 MET cc_start: 0.6678 (tpt) cc_final: 0.6450 (tpt) REVERT: P 72 MET cc_start: 0.5324 (tmm) cc_final: 0.4631 (tmm) REVERT: Q 17 ASP cc_start: 0.7211 (p0) cc_final: 0.6229 (p0) REVERT: Q 163 TYR cc_start: 0.1979 (t80) cc_final: 0.1225 (t80) REVERT: Q 192 MET cc_start: 0.3958 (mpp) cc_final: 0.3732 (mpp) REVERT: R 39 VAL cc_start: -0.1817 (OUTLIER) cc_final: -0.2166 (m) REVERT: R 165 MET cc_start: 0.6328 (tpp) cc_final: 0.6110 (tpp) REVERT: R 180 ASN cc_start: 0.7364 (p0) cc_final: 0.6798 (t0) REVERT: S 157 ASN cc_start: 0.6835 (p0) cc_final: 0.5754 (p0) REVERT: S 180 ASN cc_start: 0.5802 (p0) cc_final: 0.5103 (p0) outliers start: 89 outliers final: 59 residues processed: 725 average time/residue: 0.4055 time to fit residues: 458.6529 Evaluate side-chains 713 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 644 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 208 MET Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 479 THR Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain M residue 352 ILE Chi-restraints excluded: chain M residue 420 GLN Chi-restraints excluded: chain M residue 433 LYS Chi-restraints excluded: chain M residue 456 ASP Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 305 optimal weight: 9.9990 chunk 322 optimal weight: 0.0030 chunk 294 optimal weight: 0.4980 chunk 313 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 283 optimal weight: 0.2980 chunk 296 optimal weight: 10.0000 chunk 312 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 75 ASN C 51 GLN ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN E 121 GLN E 146 ASN ** F 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 ASN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28149 Z= 0.163 Angle : 0.643 14.949 38043 Z= 0.310 Chirality : 0.044 0.182 4287 Planarity : 0.004 0.052 4940 Dihedral : 4.284 43.475 3885 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.24 % Allowed : 26.42 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3543 helix: 0.25 (0.14), residues: 1416 sheet: -0.27 (0.24), residues: 496 loop : -1.31 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 55 HIS 0.005 0.001 HIS D 156 PHE 0.035 0.001 PHE I 102 TYR 0.032 0.001 TYR N 185 ARG 0.009 0.000 ARG N 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 658 time to evaluate : 2.969 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: A 51 LYS cc_start: 0.8790 (tppt) cc_final: 0.8453 (tptt) REVERT: A 141 SER cc_start: 0.7717 (p) cc_final: 0.7433 (p) REVERT: A 203 ARG cc_start: 0.7392 (mtt90) cc_final: 0.7080 (mtt90) REVERT: B 50 PHE cc_start: 0.8924 (t80) cc_final: 0.8721 (t80) REVERT: B 114 MET cc_start: 0.8441 (mtp) cc_final: 0.8240 (mtp) REVERT: B 118 ARG cc_start: 0.8534 (mtt90) cc_final: 0.8012 (mpt-90) REVERT: C 23 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7884 (mtm180) REVERT: C 32 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6136 (tm-30) REVERT: C 34 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7079 (mp0) REVERT: C 134 GLU cc_start: 0.7506 (tp30) cc_final: 0.7098 (tp30) REVERT: C 142 TYR cc_start: 0.8530 (t80) cc_final: 0.8249 (t80) REVERT: C 164 GLU cc_start: 0.8639 (pt0) cc_final: 0.7995 (pp20) REVERT: C 165 ASP cc_start: 0.8149 (m-30) cc_final: 0.7301 (m-30) REVERT: D 83 TYR cc_start: 0.8465 (t80) cc_final: 0.8220 (t80) REVERT: D 96 TYR cc_start: 0.7516 (t80) cc_final: 0.6793 (t80) REVERT: D 128 LEU cc_start: 0.8785 (tp) cc_final: 0.8510 (tp) REVERT: D 157 GLN cc_start: 0.7985 (mt0) cc_final: 0.7430 (mt0) REVERT: D 165 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7463 (mm-40) REVERT: D 180 LYS cc_start: 0.8660 (ttmt) cc_final: 0.7742 (ttmt) REVERT: D 222 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.7903 (tp) REVERT: E 32 GLU cc_start: 0.7064 (tp30) cc_final: 0.6769 (tp30) REVERT: E 34 GLU cc_start: 0.7436 (pt0) cc_final: 0.7093 (mm-30) REVERT: E 100 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9208 (mt) REVERT: E 108 LYS cc_start: 0.8314 (ptpt) cc_final: 0.7713 (mtmm) REVERT: E 111 SER cc_start: 0.7550 (t) cc_final: 0.7134 (t) REVERT: E 118 MET cc_start: 0.7462 (tpt) cc_final: 0.7129 (tpt) REVERT: F 154 MET cc_start: 0.7875 (tmm) cc_final: 0.7260 (ttt) REVERT: H 378 THR cc_start: 0.9443 (t) cc_final: 0.9230 (m) REVERT: H 420 GLN cc_start: 0.8425 (mt0) cc_final: 0.7830 (mt0) REVERT: H 446 THR cc_start: 0.9304 (p) cc_final: 0.9101 (t) REVERT: H 447 TYR cc_start: 0.8425 (m-80) cc_final: 0.7709 (m-80) REVERT: I 74 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8529 (pp) REVERT: I 102 PHE cc_start: 0.5737 (t80) cc_final: 0.5498 (t80) REVERT: I 146 MET cc_start: 0.7792 (mmm) cc_final: 0.7360 (mmm) REVERT: J 408 THR cc_start: 0.8497 (m) cc_final: 0.8199 (p) REVERT: K 215 MET cc_start: 0.5551 (ppp) cc_final: 0.4876 (mmm) REVERT: L 79 ILE cc_start: 0.9077 (pt) cc_final: 0.8877 (mt) REVERT: L 98 ASN cc_start: 0.8462 (m-40) cc_final: 0.7693 (t0) REVERT: L 169 GLU cc_start: 0.7552 (pp20) cc_final: 0.6576 (pp20) REVERT: L 172 ILE cc_start: 0.8703 (mt) cc_final: 0.8294 (tp) REVERT: L 173 GLU cc_start: 0.6604 (pt0) cc_final: 0.5862 (pt0) REVERT: L 179 ARG cc_start: 0.7290 (tpt170) cc_final: 0.6868 (tpt170) REVERT: M 399 GLU cc_start: 0.7747 (mp0) cc_final: 0.7257 (mp0) REVERT: M 456 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8523 (t0) REVERT: N 19 ASP cc_start: 0.7859 (p0) cc_final: 0.7523 (p0) REVERT: N 106 VAL cc_start: 0.8068 (t) cc_final: 0.7862 (t) REVERT: N 152 ARG cc_start: 0.7037 (mmt180) cc_final: 0.6658 (mmm-85) REVERT: N 181 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7607 (mm-40) REVERT: N 192 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8918 (mm) REVERT: N 199 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: N 244 ASP cc_start: 0.7105 (p0) cc_final: 0.6392 (p0) REVERT: N 250 MET cc_start: 0.7588 (tmm) cc_final: 0.7199 (tmm) REVERT: O 42 MET cc_start: 0.7734 (ptp) cc_final: 0.7343 (ptp) REVERT: O 93 ILE cc_start: 0.8677 (mp) cc_final: 0.8311 (mt) REVERT: P 16 MET cc_start: 0.6750 (tpt) cc_final: 0.6519 (tpt) REVERT: P 72 MET cc_start: 0.5353 (tmm) cc_final: 0.4636 (tmm) REVERT: Q 17 ASP cc_start: 0.7275 (p0) cc_final: 0.6260 (p0) REVERT: Q 163 TYR cc_start: 0.2070 (t80) cc_final: 0.1264 (t80) REVERT: Q 192 MET cc_start: 0.4268 (mpp) cc_final: 0.4050 (mpp) REVERT: R 8 PHE cc_start: 0.5460 (OUTLIER) cc_final: 0.5182 (m-80) REVERT: R 39 VAL cc_start: -0.1845 (OUTLIER) cc_final: -0.2230 (m) REVERT: R 165 MET cc_start: 0.6203 (tpp) cc_final: 0.5949 (tpp) REVERT: R 180 ASN cc_start: 0.7459 (p0) cc_final: 0.6942 (t0) REVERT: S 180 ASN cc_start: 0.6112 (p0) cc_final: 0.5419 (p0) outliers start: 96 outliers final: 67 residues processed: 715 average time/residue: 0.3764 time to fit residues: 422.2264 Evaluate side-chains 707 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 632 time to evaluate : 3.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain J residue 364 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 479 THR Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain K residue 209 PHE Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 352 ILE Chi-restraints excluded: chain M residue 433 LYS Chi-restraints excluded: chain M residue 456 ASP Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain R residue 8 PHE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 205 optimal weight: 2.9990 chunk 331 optimal weight: 9.9990 chunk 202 optimal weight: 0.4980 chunk 157 optimal weight: 0.9990 chunk 230 optimal weight: 0.3980 chunk 347 optimal weight: 1.9990 chunk 320 optimal weight: 9.9990 chunk 276 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN C 24 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** F 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 HIS ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 ASN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28149 Z= 0.200 Angle : 0.673 13.870 38043 Z= 0.326 Chirality : 0.045 0.167 4287 Planarity : 0.004 0.052 4940 Dihedral : 4.445 46.224 3885 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.04 % Allowed : 26.76 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3543 helix: 0.28 (0.14), residues: 1426 sheet: -0.13 (0.24), residues: 509 loop : -1.36 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 55 HIS 0.005 0.001 HIS G 120 PHE 0.041 0.001 PHE N 92 TYR 0.033 0.001 TYR N 185 ARG 0.009 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 645 time to evaluate : 3.518 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: A 51 LYS cc_start: 0.8819 (tppt) cc_final: 0.8500 (tptt) REVERT: A 141 SER cc_start: 0.7767 (p) cc_final: 0.7515 (p) REVERT: A 174 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: B 50 PHE cc_start: 0.8985 (t80) cc_final: 0.8756 (t80) REVERT: C 32 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6143 (tm-30) REVERT: C 34 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7027 (mp0) REVERT: C 121 GLN cc_start: 0.8267 (pt0) cc_final: 0.7769 (pt0) REVERT: C 164 GLU cc_start: 0.8680 (pt0) cc_final: 0.7990 (pp20) REVERT: D 83 TYR cc_start: 0.8539 (t80) cc_final: 0.8303 (t80) REVERT: D 96 TYR cc_start: 0.7572 (t80) cc_final: 0.6684 (t80) REVERT: D 128 LEU cc_start: 0.8800 (tp) cc_final: 0.8540 (tp) REVERT: D 157 GLN cc_start: 0.7866 (mt0) cc_final: 0.7632 (mt0) REVERT: D 165 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7490 (mm-40) REVERT: D 180 LYS cc_start: 0.8717 (ttmt) cc_final: 0.7837 (ttmt) REVERT: E 34 GLU cc_start: 0.7219 (pt0) cc_final: 0.6991 (mm-30) REVERT: E 100 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9240 (mt) REVERT: E 108 LYS cc_start: 0.8451 (ptpt) cc_final: 0.7846 (mtmm) REVERT: E 111 SER cc_start: 0.7861 (t) cc_final: 0.7473 (t) REVERT: E 118 MET cc_start: 0.7513 (tpt) cc_final: 0.7114 (tpt) REVERT: E 172 MET cc_start: 0.8662 (ptt) cc_final: 0.8357 (ptm) REVERT: F 154 MET cc_start: 0.7871 (tmm) cc_final: 0.7545 (ttt) REVERT: G 139 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8290 (tm-30) REVERT: H 378 THR cc_start: 0.9492 (t) cc_final: 0.9251 (m) REVERT: H 420 GLN cc_start: 0.8329 (mt0) cc_final: 0.7624 (mt0) REVERT: H 447 TYR cc_start: 0.8527 (m-80) cc_final: 0.7789 (m-80) REVERT: I 74 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8557 (pp) REVERT: I 88 SER cc_start: 0.8756 (t) cc_final: 0.8354 (m) REVERT: I 146 MET cc_start: 0.7704 (mmm) cc_final: 0.7386 (mmm) REVERT: J 408 THR cc_start: 0.8563 (m) cc_final: 0.8288 (p) REVERT: J 438 VAL cc_start: 0.9177 (m) cc_final: 0.8938 (p) REVERT: K 215 MET cc_start: 0.5683 (ppp) cc_final: 0.4739 (mmm) REVERT: L 98 ASN cc_start: 0.8366 (m110) cc_final: 0.7861 (t0) REVERT: L 169 GLU cc_start: 0.7628 (pp20) cc_final: 0.6495 (pp20) REVERT: L 172 ILE cc_start: 0.8744 (mt) cc_final: 0.8312 (tp) REVERT: L 173 GLU cc_start: 0.6740 (pt0) cc_final: 0.5900 (pt0) REVERT: L 179 ARG cc_start: 0.7304 (tpt170) cc_final: 0.6863 (tpt170) REVERT: M 399 GLU cc_start: 0.7819 (mp0) cc_final: 0.7373 (mp0) REVERT: M 456 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8553 (t0) REVERT: N 19 ASP cc_start: 0.7853 (p0) cc_final: 0.7546 (p0) REVERT: N 47 GLU cc_start: 0.8488 (tp30) cc_final: 0.8120 (tp30) REVERT: N 143 GLN cc_start: 0.8364 (tt0) cc_final: 0.8120 (tt0) REVERT: N 152 ARG cc_start: 0.7062 (mmt180) cc_final: 0.6610 (mmm-85) REVERT: N 244 ASP cc_start: 0.7168 (p0) cc_final: 0.6440 (p0) REVERT: N 250 MET cc_start: 0.7656 (tmm) cc_final: 0.7276 (tmm) REVERT: O 93 ILE cc_start: 0.8704 (mp) cc_final: 0.8347 (mt) REVERT: P 16 MET cc_start: 0.6666 (tpt) cc_final: 0.6426 (tpt) REVERT: P 22 ARG cc_start: 0.1122 (ttp-170) cc_final: 0.0820 (ttp-170) REVERT: P 72 MET cc_start: 0.5414 (tmm) cc_final: 0.4825 (tmm) REVERT: Q 163 TYR cc_start: 0.2201 (t80) cc_final: 0.1341 (t80) REVERT: R 39 VAL cc_start: -0.1668 (OUTLIER) cc_final: -0.2032 (m) REVERT: R 165 MET cc_start: 0.6235 (tpp) cc_final: 0.5974 (tpp) REVERT: R 180 ASN cc_start: 0.7503 (p0) cc_final: 0.6982 (t0) REVERT: S 157 ASN cc_start: 0.6861 (p0) cc_final: 0.5802 (p0) REVERT: S 159 THR cc_start: 0.5184 (m) cc_final: 0.4795 (p) outliers start: 90 outliers final: 70 residues processed: 701 average time/residue: 0.4097 time to fit residues: 450.9515 Evaluate side-chains 713 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 638 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 174 GLN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 120 HIS Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 165 TYR Chi-restraints excluded: chain J residue 364 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 423 ASP Chi-restraints excluded: chain J residue 462 TYR Chi-restraints excluded: chain J residue 473 LEU Chi-restraints excluded: chain J residue 479 THR Chi-restraints excluded: chain K residue 5 HIS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 75 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain K residue 186 ASN Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 433 LYS Chi-restraints excluded: chain M residue 456 ASP Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 37 GLU Chi-restraints excluded: chain O residue 116 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 132 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain S residue 55 LYS Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 219 optimal weight: 0.4980 chunk 294 optimal weight: 0.0470 chunk 84 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 overall best weight: 3.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN C 24 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN E 121 GLN ** F 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 ASN ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.103298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.093954 restraints weight = 101341.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.095698 restraints weight = 53206.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.096847 restraints weight = 31896.046| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 28149 Z= 0.297 Angle : 0.798 59.098 38043 Z= 0.411 Chirality : 0.047 0.369 4287 Planarity : 0.004 0.060 4940 Dihedral : 4.448 46.766 3885 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.14 % Allowed : 27.09 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3543 helix: 0.25 (0.14), residues: 1427 sheet: -0.10 (0.24), residues: 513 loop : -1.39 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 208 HIS 0.006 0.001 HIS F 179 PHE 0.026 0.002 PHE N 92 TYR 0.030 0.001 TYR N 185 ARG 0.022 0.001 ARG B 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7739.12 seconds wall clock time: 139 minutes 44.87 seconds (8384.87 seconds total)