Starting phenix.real_space_refine on Thu Apr 11 11:53:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eko_31171/04_2024/7eko_31171.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eko_31171/04_2024/7eko_31171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eko_31171/04_2024/7eko_31171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eko_31171/04_2024/7eko_31171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eko_31171/04_2024/7eko_31171.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eko_31171/04_2024/7eko_31171.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 153 5.16 5 C 14214 2.51 5 N 3853 2.21 5 O 4250 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 GLU 153": "OE1" <-> "OE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 165": "OD1" <-> "OD2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E ASP 76": "OD1" <-> "OD2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F ASP 201": "OD1" <-> "OD2" Residue "F PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G GLU 191": "OE1" <-> "OE2" Residue "H GLU 404": "OE1" <-> "OE2" Residue "H GLU 476": "OE1" <-> "OE2" Residue "I PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 90": "OD1" <-> "OD2" Residue "I PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 367": "OD1" <-> "OD2" Residue "J PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 467": "OE1" <-> "OE2" Residue "J TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "K ASP 211": "OD1" <-> "OD2" Residue "K GLU 228": "OE1" <-> "OE2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "L TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 221": "OD1" <-> "OD2" Residue "M PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 399": "OE1" <-> "OE2" Residue "M GLU 467": "OE1" <-> "OE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ASP 80": "OD1" <-> "OD2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 159": "NH1" <-> "NH2" Residue "N ASP 198": "OD1" <-> "OD2" Residue "N GLU 202": "OE1" <-> "OE2" Residue "N ASP 206": "OD1" <-> "OD2" Residue "N GLU 209": "OE1" <-> "OE2" Residue "N GLU 224": "OE1" <-> "OE2" Residue "N GLU 232": "OE1" <-> "OE2" Residue "N TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 311": "OE1" <-> "OE2" Residue "N TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O GLU 34": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 66": "OD1" <-> "OD2" Residue "O PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 121": "OE1" <-> "OE2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O ASP 135": "OD1" <-> "OD2" Residue "O PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22470 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1728 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 9, 'TRANS': 212} 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: {'PTRANS': 14, 'TRANS': 218} 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} Time building chain proxies: 11.47, per 1000 atoms: 0.51 Number of scatterers: 22470 At special positions: 0 Unit cell: (166.068, 123.892, 122.574, 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 153 16.00 O 4250 8.00 N 3853 7.00 C 14214 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: 7.97 Conformation dependent library (CDL) restraints added in 4.3 seconds 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5316 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 35 sheets defined 53.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 49 through 67 Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.508A pdb=" N LEU A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 171 Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.557A pdb=" N VAL A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 60 Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 166 through 192 Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 34 through 52 removed outlier: 3.743A pdb=" N ASP C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 81 removed outlier: 3.655A pdb=" N CYS C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 130 through 156 Processing helix chain 'C' and resid 158 through 168 removed outlier: 4.456A pdb=" N ARG C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'D' and resid 43 through 59 Processing helix chain 'D' and resid 70 through 88 removed outlier: 3.710A pdb=" N ASP D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 117 Processing helix chain 'D' and resid 132 through 140 Processing helix chain 'D' and resid 166 through 192 Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 34 through 52 Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 96 through 103 Processing helix chain 'E' and resid 129 through 155 Processing helix chain 'E' and resid 158 through 167 removed outlier: 3.516A pdb=" N ILE E 162 " --> pdb=" O PRO E 158 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 70 through 88 Processing helix chain 'F' and resid 103 through 117 Processing helix chain 'F' and resid 132 through 139 Processing helix chain 'F' and resid 165 through 192 Processing helix chain 'F' and resid 194 through 204 removed outlier: 3.892A pdb=" N ARG F 204 " --> pdb=" O LYS F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'G' and resid 18 through 24 Processing helix chain 'G' and resid 34 through 52 Processing helix chain 'G' and resid 67 through 81 Processing helix chain 'G' and resid 96 through 103 Processing helix chain 'G' and resid 130 through 156 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 173 through 181 Processing helix chain 'H' and resid 358 through 372 removed outlier: 3.504A pdb=" N GLY H 362 " --> pdb=" O SER H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 394 Processing helix chain 'H' and resid 420 through 447 Processing helix chain 'H' and resid 449 through 457 Processing helix chain 'H' and resid 464 through 472 Processing helix chain 'H' and resid 479 through 492 removed outlier: 4.000A pdb=" N MET H 483 " --> pdb=" O THR H 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 20 Processing helix chain 'I' and resid 21 through 23 No H-bonds generated for 'chain 'I' and resid 21 through 23' Processing helix chain 'I' and resid 27 through 35 Processing helix chain 'I' and resid 45 through 60 Processing helix chain 'I' and resid 89 through 102 removed outlier: 4.335A pdb=" N PHE I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 125 Processing helix chain 'I' and resid 152 through 179 Processing helix chain 'I' and resid 181 through 189 Processing helix chain 'I' and resid 197 through 204 Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'J' and resid 358 through 372 removed outlier: 3.684A pdb=" N ILE J 372 " --> pdb=" O ALA J 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 394 Processing helix chain 'J' and resid 420 through 447 Processing helix chain 'J' and resid 449 through 459 removed outlier: 3.548A pdb=" N ARG J 459 " --> pdb=" O ARG J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 472 Processing helix chain 'J' and resid 479 through 509 removed outlier: 4.036A pdb=" N TYR J 496 " --> pdb=" O GLN J 492 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS J 497 " --> pdb=" O VAL J 493 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 19 through 27 Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.595A pdb=" N ALA K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 93 removed outlier: 3.532A pdb=" N ILE K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 142 through 144 No H-bonds generated for 'chain 'K' and resid 142 through 144' Processing helix chain 'K' and resid 145 through 169 removed outlier: 3.602A pdb=" N ARG K 150 " --> pdb=" O ILE K 146 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS K 151 " --> pdb=" O ASP K 147 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU K 155 " --> pdb=" O LYS K 151 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 180 removed outlier: 4.032A pdb=" N THR K 180 " --> pdb=" O MET K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 194 Processing helix chain 'K' and resid 210 through 214 Processing helix chain 'L' and resid 53 through 60 Processing helix chain 'L' and resid 71 through 89 removed outlier: 3.707A pdb=" N ASP L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 117 Processing helix chain 'L' and resid 131 through 137 Processing helix chain 'L' and resid 166 through 193 removed outlier: 3.510A pdb=" N MET L 170 " --> pdb=" O GLN L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 204 removed outlier: 3.742A pdb=" N SER L 204 " --> pdb=" O ILE L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 217 Processing helix chain 'M' and resid 358 through 372 removed outlier: 3.878A pdb=" N ILE M 372 " --> pdb=" O ALA M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 394 removed outlier: 3.934A pdb=" N ALA M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 447 Processing helix chain 'M' and resid 449 through 458 Processing helix chain 'M' and resid 464 through 472 Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 37 through 54 Processing helix chain 'N' and resid 81 through 93 Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'N' and resid 143 through 169 removed outlier: 3.541A pdb=" N VAL N 147 " --> pdb=" O GLN N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 181 removed outlier: 3.513A pdb=" N GLN N 181 " --> pdb=" O ASP N 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 195 Processing helix chain 'N' and resid 204 through 218 Processing helix chain 'N' and resid 225 through 261 removed outlier: 3.796A pdb=" N GLN N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 277 removed outlier: 3.522A pdb=" N ASN N 272 " --> pdb=" O ASN N 268 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN N 277 " --> pdb=" O MET N 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 283 removed outlier: 4.236A pdb=" N LEU N 283 " --> pdb=" O LYS N 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 1 through 5 Processing helix chain 'O' and resid 7 through 12 Processing helix chain 'O' and resid 16 through 33 Processing helix chain 'O' and resid 39 through 50 Processing helix chain 'O' and resid 53 through 63 Processing helix chain 'O' and resid 66 through 80 Processing helix chain 'O' and resid 96 through 113 Processing helix chain 'O' and resid 119 through 129 Processing helix chain 'O' and resid 137 through 141 removed outlier: 3.525A pdb=" N ASN O 141 " --> pdb=" O PRO O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 removed outlier: 6.528A pdb=" N ILE A 72 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL A 103 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 105 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE A 76 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA A 107 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 45 removed outlier: 6.528A pdb=" N ILE A 72 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL A 103 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 105 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE A 76 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ALA A 107 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N TYR A 125 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR A 102 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET A 127 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA A 104 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA A 126 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 143 removed outlier: 7.116A pdb=" N GLY A 139 " --> pdb=" O PHE I 150 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE I 150 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER A 141 " --> pdb=" O ARG I 148 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG I 148 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 66 removed outlier: 5.609A pdb=" N SER B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 128 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG B 152 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY B 127 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N MET B 154 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA B 129 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 155 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 206 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 66 removed outlier: 5.609A pdb=" N SER B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 128 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 165 Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 30 removed outlier: 5.837A pdb=" N SER C 63 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 92 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ARG C 116 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY C 91 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N MET C 118 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 93 " --> pdb=" O MET C 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AA9, first strand: chain 'D' and resid 62 through 66 removed outlier: 6.243A pdb=" N VAL D 63 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN D 98 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 65 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 12.569A pdb=" N ILE D 93 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 13.530A pdb=" N ILE D 126 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N MET D 95 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N LEU D 128 " --> pdb=" O MET D 95 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL D 97 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA D 130 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER D 99 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N MET D 154 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA D 129 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 62 through 66 removed outlier: 6.243A pdb=" N VAL D 63 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN D 98 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 65 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 12.569A pdb=" N ILE D 93 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 13.530A pdb=" N ILE D 126 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N MET D 95 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N LEU D 128 " --> pdb=" O MET D 95 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL D 97 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA D 130 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER D 99 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR D 146 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR D 123 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 159 through 165 removed outlier: 4.060A pdb=" N GLY M 419 " --> pdb=" O GLY D 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 26 through 30 removed outlier: 3.626A pdb=" N ASN E 62 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE E 57 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR E 88 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 59 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE E 61 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU E 92 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG E 116 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N GLY E 91 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N MET E 118 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA E 93 " --> pdb=" O MET E 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 26 through 30 removed outlier: 3.626A pdb=" N ASN E 62 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE E 57 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR E 88 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 59 " --> pdb=" O TYR E 88 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE E 61 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU E 92 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ASN E 110 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 6.174A 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: 6.592A pdb=" N VAL F 63 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ASN F 98 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU F 65 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 93 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N CYS F 124 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N MET F 95 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE F 126 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL F 97 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU F 128 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG F 152 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY F 127 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N MET F 154 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA F 129 " --> pdb=" O MET F 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 62 through 66 removed outlier: 6.592A pdb=" N VAL F 63 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ASN F 98 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU F 65 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 93 " --> pdb=" O SER F 122 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N CYS F 124 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N MET F 95 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE F 126 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL F 97 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU F 128 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 221 " --> pdb=" O ARG F 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 26 through 30 removed outlier: 6.203A pdb=" N ILE G 57 " --> pdb=" O ASN G 86 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TYR G 88 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE G 59 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE G 61 " --> pdb=" O PHE G 90 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU G 92 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG G 116 " --> pdb=" O CYS G 89 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY G 91 " --> pdb=" O ARG G 116 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET G 118 " --> pdb=" O GLY G 91 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA G 93 " --> pdb=" O MET G 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 26 through 30 removed outlier: 6.203A pdb=" N ILE G 57 " --> pdb=" O ASN G 86 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TYR G 88 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE G 59 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE G 61 " --> pdb=" O PHE G 90 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU G 92 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN G 110 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N THR G 87 " --> pdb=" O ASN G 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 125 through 129 removed outlier: 3.561A pdb=" N ALA G 126 " --> pdb=" O LEU J 417 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 347 through 354 removed outlier: 5.494A pdb=" N SER H 354 " --> pdb=" O LEU H 381 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL H 383 " --> pdb=" O SER H 354 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS H 407 " --> pdb=" O ALA H 380 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY H 382 " --> pdb=" O HIS H 407 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N MET H 409 " --> pdb=" O GLY H 382 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA H 384 " --> pdb=" O MET H 409 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 347 through 354 removed outlier: 5.494A pdb=" N SER H 354 " --> pdb=" O LEU H 381 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL H 383 " --> pdb=" O SER H 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 37 through 40 removed outlier: 5.901A pdb=" N ILE I 70 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY I 110 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL I 72 " --> pdb=" O GLY I 110 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR I 112 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU I 74 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS I 114 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LYS I 138 " --> pdb=" O VAL I 111 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP I 113 " --> pdb=" O LYS I 138 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER I 140 " --> pdb=" O TRP I 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA I 115 " --> pdb=" O SER I 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 37 through 40 removed outlier: 5.901A pdb=" N ILE I 70 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY I 110 " --> pdb=" O ILE I 70 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL I 72 " --> pdb=" O GLY I 110 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR I 112 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU I 74 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS I 114 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N TYR I 132 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR I 109 " --> pdb=" O TYR I 132 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG I 131 " --> pdb=" O LYS I 209 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 348 through 354 removed outlier: 6.306A pdb=" N VAL J 348 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU J 379 " --> pdb=" O VAL J 348 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N MET J 350 " --> pdb=" O LEU J 379 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU J 381 " --> pdb=" O MET J 350 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE J 352 " --> pdb=" O LEU J 381 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL J 383 " --> pdb=" O ILE J 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER J 354 " --> pdb=" O VAL J 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 348 through 354 removed outlier: 6.306A pdb=" N VAL J 348 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU J 379 " --> pdb=" O VAL J 348 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N MET J 350 " --> pdb=" O LEU J 379 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU J 381 " --> pdb=" O MET J 350 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE J 352 " --> pdb=" O LEU J 381 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL J 383 " --> pdb=" O ILE J 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER J 354 " --> pdb=" O VAL J 383 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLY J 382 " --> pdb=" O THR J 403 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG J 400 " --> pdb=" O GLU J 476 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA J 478 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL J 402 " --> pdb=" O ALA J 478 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.227A pdb=" N ILE K 59 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU K 100 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE K 61 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL K 102 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE K 63 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN K 104 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR K 128 " --> pdb=" O CYS K 101 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY K 103 " --> pdb=" O THR K 128 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N MET K 130 " --> pdb=" O GLY K 103 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA K 105 " --> pdb=" O MET K 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.227A pdb=" N ILE K 59 " --> pdb=" O TYR K 98 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU K 100 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE K 61 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL K 102 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE K 63 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN K 104 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA K 122 " --> pdb=" O ILE K 97 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR K 99 " --> pdb=" O ALA K 122 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU K 124 " --> pdb=" O THR K 99 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N CYS K 101 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA K 123 " --> 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 64 through 66 removed outlier: 6.102A pdb=" N ILE L 93 " --> pdb=" O ALA L 122 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL L 124 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 5.957A 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 130 removed outlier: 6.522A pdb=" N CYS L 129 " --> pdb=" O MET L 155 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 147 through 148 Processing sheet with id=AD4, first strand: chain 'M' and resid 348 through 354 removed outlier: 6.126A pdb=" N VAL M 348 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU M 379 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET M 350 " --> pdb=" O LEU M 379 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU M 381 " --> pdb=" O MET M 350 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE M 352 " --> pdb=" O LEU M 381 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL M 383 " --> pdb=" O ILE M 352 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N HIS M 407 " --> pdb=" O ALA M 380 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY M 382 " --> pdb=" O HIS M 407 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N MET M 409 " --> pdb=" O GLY M 382 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA M 384 " --> pdb=" O MET M 409 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 348 through 354 removed outlier: 6.126A pdb=" N VAL M 348 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU M 379 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET M 350 " --> pdb=" O LEU M 379 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU M 381 " --> pdb=" O MET M 350 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE M 352 " --> pdb=" O LEU M 381 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL M 383 " --> pdb=" O ILE M 352 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.106A pdb=" N ILE N 60 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL N 100 " --> pdb=" O ILE N 60 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N MET N 62 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET N 102 " --> pdb=" O MET N 62 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE N 64 " --> pdb=" O MET N 102 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU N 104 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS N 122 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR N 99 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 129 through 131 Processing sheet with id=AD8, first strand: chain 'O' and resid 37 through 38 1273 hydrogen bonds defined for protein. 3726 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: 7.88 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6792 1.33 - 1.46: 4819 1.46 - 1.58: 11004 1.58 - 1.71: 0 1.71 - 1.83: 272 Bond restraints: 22887 Sorted by residual: bond pdb=" C GLY A 81 " pdb=" N GLN A 82 " ideal model delta sigma weight residual 1.327 1.266 0.061 1.61e-02 3.86e+03 1.43e+01 bond pdb=" N ILE K 59 " pdb=" CA ILE K 59 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.62e+00 bond pdb=" N GLN K 133 " pdb=" CA GLN K 133 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.16e-02 7.43e+03 9.56e+00 bond pdb=" N VAL G 193 " pdb=" CA VAL G 193 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.08e-02 8.57e+03 9.49e+00 bond pdb=" N VAL O 80 " pdb=" CA VAL O 80 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.15e+00 ... (remaining 22882 not shown) Histogram of bond angle deviations from ideal: 95.75 - 104.36: 418 104.36 - 112.97: 12257 112.97 - 121.58: 13410 121.58 - 130.20: 4750 130.20 - 138.81: 94 Bond angle restraints: 30929 Sorted by residual: angle pdb=" C GLY N 170 " pdb=" N LEU N 171 " pdb=" CA LEU N 171 " ideal model delta sigma weight residual 120.97 138.81 -17.84 2.84e+00 1.24e-01 3.95e+01 angle pdb=" N LEU O 84 " pdb=" CA LEU O 84 " pdb=" C LEU O 84 " ideal model delta sigma weight residual 112.72 105.87 6.85 1.14e+00 7.69e-01 3.62e+01 angle pdb=" CB MET H 483 " pdb=" CG MET H 483 " pdb=" SD MET H 483 " ideal model delta sigma weight residual 112.70 95.79 16.91 3.00e+00 1.11e-01 3.18e+01 angle pdb=" N PRO K 56 " pdb=" CA PRO K 56 " pdb=" C PRO K 56 " ideal model delta sigma weight residual 114.68 109.09 5.59 1.04e+00 9.25e-01 2.89e+01 angle pdb=" N PRO K 58 " pdb=" CA PRO K 58 " pdb=" C PRO K 58 " ideal model delta sigma weight residual 111.22 118.12 -6.90 1.40e+00 5.10e-01 2.43e+01 ... (remaining 30924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 12883 23.98 - 47.95: 823 47.95 - 71.93: 148 71.93 - 95.90: 19 95.90 - 119.88: 1 Dihedral angle restraints: 13874 sinusoidal: 5564 harmonic: 8310 Sorted by residual: dihedral pdb=" CA PRO K 134 " pdb=" C PRO K 134 " pdb=" N LEU K 135 " pdb=" CA LEU K 135 " ideal model delta harmonic sigma weight residual -180.00 -60.12 -119.88 0 5.00e+00 4.00e-02 5.75e+02 dihedral pdb=" CA MET H 483 " pdb=" C MET H 483 " pdb=" N HIS H 484 " pdb=" CA HIS H 484 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ILE F 223 " pdb=" C ILE F 223 " pdb=" N SER F 224 " pdb=" CA SER F 224 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 13871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2962 0.079 - 0.159: 418 0.159 - 0.238: 55 0.238 - 0.317: 5 0.317 - 0.396: 3 Chirality restraints: 3443 Sorted by residual: chirality pdb=" CG LEU J 417 " pdb=" CB LEU J 417 " pdb=" CD1 LEU J 417 " pdb=" CD2 LEU J 417 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA VAL L 124 " pdb=" N VAL L 124 " pdb=" C VAL L 124 " pdb=" CB VAL L 124 " both_signs ideal model delta sigma weight residual False 2.44 2.78 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA GLU A 25 " pdb=" N GLU A 25 " pdb=" C GLU A 25 " pdb=" CB GLU A 25 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3440 not shown) Planarity restraints: 4017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 110 " 0.028 2.00e-02 2.50e+03 5.57e-02 3.11e+01 pdb=" C SER A 110 " -0.096 2.00e-02 2.50e+03 pdb=" O SER A 110 " 0.034 2.00e-02 2.50e+03 pdb=" N TYR A 111 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 52 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO E 53 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO E 53 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 53 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 223 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ILE F 223 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE F 223 " 0.024 2.00e-02 2.50e+03 pdb=" N SER F 224 " 0.021 2.00e-02 2.50e+03 ... (remaining 4014 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 440 2.68 - 3.23: 22304 3.23 - 3.79: 35651 3.79 - 4.34: 47994 4.34 - 4.90: 79458 Nonbonded interactions: 185847 Sorted by model distance: nonbonded pdb=" OH TYR I 195 " pdb=" OE2 GLU J 430 " model vdw 2.119 2.440 nonbonded pdb=" O SER L 163 " pdb=" NH1 ARG L 164 " model vdw 2.120 2.520 nonbonded pdb=" OG SER A 141 " pdb=" CB ALA I 156 " model vdw 2.127 3.460 nonbonded pdb=" OD1 ASN C 146 " pdb=" NH2 ARG C 149 " model vdw 2.129 2.520 nonbonded pdb=" OE1 GLN C 121 " pdb=" NZ LYS C 144 " model vdw 2.134 2.520 ... (remaining 185842 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.520 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 58.410 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.009 0.080 22887 Z= 0.598 Angle : 0.987 17.838 30929 Z= 0.590 Chirality : 0.058 0.396 3443 Planarity : 0.005 0.113 4017 Dihedral : 15.699 119.881 8558 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.08 % Favored : 93.85 % Rotamer: Outliers : 2.55 % Allowed : 1.67 % Favored : 95.78 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2860 helix: 0.16 (0.13), residues: 1536 sheet: -0.91 (0.31), residues: 282 loop : -1.69 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 225 HIS 0.020 0.003 HIS H 484 PHE 0.028 0.003 PHE I 196 TYR 0.030 0.003 TYR K 149 ARG 0.011 0.001 ARG I 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 518 time to evaluate : 2.589 Fit side-chains REVERT: A 138 MET cc_start: 0.7430 (mmt) cc_final: 0.6851 (mmt) REVERT: E 78 MET cc_start: 0.8592 (mtm) cc_final: 0.7991 (mtm) REVERT: E 141 MET cc_start: 0.7651 (mmm) cc_final: 0.7445 (mmt) REVERT: E 161 LYS cc_start: 0.6856 (pttp) cc_final: 0.6247 (mttt) REVERT: F 207 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5403 (t80) REVERT: G 34 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5718 (pm20) REVERT: G 163 GLU cc_start: 0.6260 (mm-30) cc_final: 0.5477 (pt0) REVERT: G 180 TYR cc_start: 0.7744 (t80) cc_final: 0.7515 (t80) REVERT: H 460 ASP cc_start: 0.7476 (m-30) cc_final: 0.7229 (m-30) REVERT: I 183 GLU cc_start: 0.8138 (tp30) cc_final: 0.7756 (tp30) REVERT: J 464 THR cc_start: 0.6401 (m) cc_final: 0.6199 (m) REVERT: J 468 THR cc_start: 0.8649 (m) cc_final: 0.8406 (m) REVERT: K 108 GLU cc_start: 0.6207 (mp0) cc_final: 0.5903 (mp0) REVERT: K 155 GLU cc_start: 0.4788 (tt0) cc_final: 0.4172 (tt0) REVERT: K 169 LYS cc_start: 0.6287 (OUTLIER) cc_final: 0.5866 (pttp) REVERT: L 132 MET cc_start: 0.8126 (mmp) cc_final: 0.7800 (mmm) REVERT: L 216 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6482 (tm-30) REVERT: N 23 LEU cc_start: 0.8647 (tp) cc_final: 0.8240 (tp) REVERT: O 94 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7262 (ttpp) REVERT: O 145 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6033 (mp0) outliers start: 61 outliers final: 8 residues processed: 555 average time/residue: 0.3783 time to fit residues: 313.4444 Evaluate side-chains 459 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 447 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain K residue 169 LYS Chi-restraints excluded: chain M residue 428 SER Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 94 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 157 GLN D 51 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN G 44 GLN G 120 HIS G 121 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN I 136 HIS ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 497 HIS ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 ASN L 206 ASN M 451 HIS N 229 GLN O 113 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22887 Z= 0.210 Angle : 0.615 9.762 30929 Z= 0.320 Chirality : 0.042 0.188 3443 Planarity : 0.005 0.089 4017 Dihedral : 5.845 57.063 3180 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.88 % Allowed : 8.48 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 2860 helix: 1.03 (0.13), residues: 1547 sheet: -0.42 (0.34), residues: 224 loop : -1.38 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 112 HIS 0.010 0.001 HIS J 411 PHE 0.021 0.002 PHE I 102 TYR 0.031 0.002 TYR E 154 ARG 0.008 0.000 ARG L 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 469 time to evaluate : 2.605 Fit side-chains REVERT: A 164 ARG cc_start: 0.8368 (mpt180) cc_final: 0.7968 (mmm-85) REVERT: A 172 MET cc_start: 0.8046 (mtp) cc_final: 0.7835 (mtm) REVERT: B 170 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: B 215 GLU cc_start: 0.6409 (mt-10) cc_final: 0.5346 (mt-10) REVERT: C 82 ARG cc_start: 0.6059 (mtm-85) cc_final: 0.5857 (mtm110) REVERT: C 149 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7812 (ttp80) REVERT: E 78 MET cc_start: 0.8486 (mtm) cc_final: 0.8218 (mtm) REVERT: F 207 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.5237 (t80) REVERT: G 151 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6748 (mtp) REVERT: G 163 GLU cc_start: 0.6372 (mm-30) cc_final: 0.5700 (pt0) REVERT: H 350 MET cc_start: 0.8411 (ttt) cc_final: 0.8094 (ttt) REVERT: H 460 ASP cc_start: 0.7334 (m-30) cc_final: 0.7133 (m-30) REVERT: H 489 MET cc_start: 0.5871 (mtp) cc_final: 0.5294 (mtm) REVERT: I 158 LEU cc_start: 0.7462 (mp) cc_final: 0.7135 (mt) REVERT: I 183 GLU cc_start: 0.8014 (tp30) cc_final: 0.7740 (tp30) REVERT: J 407 HIS cc_start: 0.6353 (m90) cc_final: 0.5774 (m-70) REVERT: J 480 ASN cc_start: 0.7854 (m-40) cc_final: 0.7478 (m-40) REVERT: K 108 GLU cc_start: 0.6124 (mp0) cc_final: 0.5863 (mp0) REVERT: K 193 TYR cc_start: 0.6110 (t80) cc_final: 0.5844 (t80) REVERT: L 132 MET cc_start: 0.8310 (mmp) cc_final: 0.7963 (mmm) REVERT: L 209 MET cc_start: 0.8285 (mtm) cc_final: 0.8082 (mtt) REVERT: L 216 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6461 (tm-30) REVERT: N 23 LEU cc_start: 0.8379 (tp) cc_final: 0.8091 (tp) REVERT: O 51 GLU cc_start: 0.6547 (mm-30) cc_final: 0.6145 (mt-10) REVERT: O 148 ARG cc_start: 0.6378 (tmt-80) cc_final: 0.5104 (ttp-170) outliers start: 45 outliers final: 26 residues processed: 495 average time/residue: 0.3811 time to fit residues: 294.5490 Evaluate side-chains 467 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 438 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 428 SER Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 256 optimal weight: 0.7980 chunk 277 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 205 optimal weight: 0.0060 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN G 44 GLN G 120 HIS ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22887 Z= 0.177 Angle : 0.555 11.643 30929 Z= 0.287 Chirality : 0.041 0.219 3443 Planarity : 0.004 0.065 4017 Dihedral : 5.115 54.955 3165 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.88 % Allowed : 11.11 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2860 helix: 1.50 (0.13), residues: 1556 sheet: -0.07 (0.35), residues: 224 loop : -1.18 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 112 HIS 0.013 0.001 HIS H 484 PHE 0.026 0.001 PHE I 102 TYR 0.025 0.001 TYR E 154 ARG 0.006 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 473 time to evaluate : 2.422 Fit side-chains revert: symmetry clash REVERT: A 164 ARG cc_start: 0.8388 (mpt180) cc_final: 0.7979 (mmm-85) REVERT: A 199 ASP cc_start: 0.8020 (m-30) cc_final: 0.7726 (m-30) REVERT: B 51 GLN cc_start: 0.7211 (tm-30) cc_final: 0.6960 (tm-30) REVERT: B 170 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: B 215 GLU cc_start: 0.6454 (mt-10) cc_final: 0.5287 (mt-10) REVERT: B 223 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8608 (mt) REVERT: D 200 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8331 (ttpp) REVERT: E 78 MET cc_start: 0.8525 (mtm) cc_final: 0.8251 (mtm) REVERT: E 112 MET cc_start: 0.7468 (mmp) cc_final: 0.7254 (mmt) REVERT: F 207 PHE cc_start: 0.6128 (OUTLIER) cc_final: 0.5464 (t80) REVERT: G 72 MET cc_start: 0.8617 (mmt) cc_final: 0.8178 (mmt) REVERT: G 151 MET cc_start: 0.7419 (mtp) cc_final: 0.6533 (mtp) REVERT: H 350 MET cc_start: 0.8453 (ttt) cc_final: 0.8236 (ttt) REVERT: H 489 MET cc_start: 0.5922 (mtp) cc_final: 0.5460 (mtm) REVERT: I 158 LEU cc_start: 0.7421 (mp) cc_final: 0.7217 (mt) REVERT: I 183 GLU cc_start: 0.7868 (tp30) cc_final: 0.7613 (tp30) REVERT: J 480 ASN cc_start: 0.7684 (m-40) cc_final: 0.7262 (m-40) REVERT: K 108 GLU cc_start: 0.6409 (mp0) cc_final: 0.6185 (mp0) REVERT: K 155 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5286 (mm-30) REVERT: K 193 TYR cc_start: 0.6128 (t80) cc_final: 0.5825 (t80) REVERT: L 170 MET cc_start: 0.6356 (mmm) cc_final: 0.5647 (mtt) REVERT: L 216 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6436 (tm-30) REVERT: M 432 MET cc_start: 0.7773 (mmp) cc_final: 0.7495 (mmm) REVERT: N 94 LYS cc_start: 0.6579 (pttm) cc_final: 0.5980 (ptpp) REVERT: O 51 GLU cc_start: 0.6647 (mm-30) cc_final: 0.6125 (mt-10) outliers start: 45 outliers final: 28 residues processed: 499 average time/residue: 0.3559 time to fit residues: 273.7824 Evaluate side-chains 493 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 461 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS F 189 GLN G 44 GLN G 120 HIS ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22887 Z= 0.280 Angle : 0.581 7.251 30929 Z= 0.300 Chirality : 0.042 0.162 3443 Planarity : 0.004 0.057 4017 Dihedral : 5.057 53.944 3161 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.38 % Allowed : 13.07 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2860 helix: 1.53 (0.13), residues: 1555 sheet: 0.02 (0.34), residues: 232 loop : -1.21 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 11 HIS 0.019 0.001 HIS H 484 PHE 0.016 0.002 PHE I 102 TYR 0.028 0.002 TYR C 154 ARG 0.006 0.000 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 474 time to evaluate : 2.514 Fit side-chains REVERT: A 164 ARG cc_start: 0.8417 (mpt180) cc_final: 0.7993 (mmm-85) REVERT: A 199 ASP cc_start: 0.8036 (m-30) cc_final: 0.7714 (m-30) REVERT: B 170 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: B 215 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5655 (mt-10) REVERT: B 223 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8606 (mt) REVERT: F 207 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.5934 (t80) REVERT: G 72 MET cc_start: 0.8628 (mmt) cc_final: 0.8186 (mmt) REVERT: G 151 MET cc_start: 0.7307 (mtp) cc_final: 0.6535 (mtp) REVERT: H 489 MET cc_start: 0.5959 (mtp) cc_final: 0.5543 (mtm) REVERT: I 158 LEU cc_start: 0.7594 (mp) cc_final: 0.7313 (mt) REVERT: J 480 ASN cc_start: 0.7738 (m-40) cc_final: 0.7326 (m-40) REVERT: K 108 GLU cc_start: 0.6529 (mp0) cc_final: 0.6322 (mp0) REVERT: K 155 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5482 (mm-30) REVERT: K 193 TYR cc_start: 0.6123 (t80) cc_final: 0.5793 (t80) REVERT: L 216 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6353 (tm-30) REVERT: O 51 GLU cc_start: 0.6373 (mt-10) cc_final: 0.5856 (mt-10) outliers start: 57 outliers final: 43 residues processed: 506 average time/residue: 0.3741 time to fit residues: 291.5708 Evaluate side-chains 504 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 457 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 207 PHE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 202 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN G 44 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22887 Z= 0.287 Angle : 0.582 7.239 30929 Z= 0.301 Chirality : 0.042 0.151 3443 Planarity : 0.004 0.054 4017 Dihedral : 5.042 52.372 3161 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.09 % Allowed : 14.28 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2860 helix: 1.53 (0.13), residues: 1557 sheet: 0.01 (0.34), residues: 232 loop : -1.26 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 55 HIS 0.018 0.001 HIS H 484 PHE 0.018 0.002 PHE I 102 TYR 0.026 0.002 TYR C 154 ARG 0.007 0.000 ARG N 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 447 time to evaluate : 2.711 Fit side-chains REVERT: A 164 ARG cc_start: 0.8416 (mpt180) cc_final: 0.8002 (mmm-85) REVERT: A 199 ASP cc_start: 0.8043 (m-30) cc_final: 0.7733 (m-30) REVERT: B 170 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: B 215 GLU cc_start: 0.6694 (mt-10) cc_final: 0.5639 (mt-10) REVERT: B 223 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8606 (mt) REVERT: F 195 MET cc_start: 0.7033 (mmt) cc_final: 0.6684 (mmm) REVERT: F 207 PHE cc_start: 0.6906 (m-80) cc_final: 0.6620 (m-80) REVERT: G 72 MET cc_start: 0.8597 (mmt) cc_final: 0.8132 (mmt) REVERT: G 101 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8663 (tp) REVERT: G 151 MET cc_start: 0.7247 (mtp) cc_final: 0.6567 (mtp) REVERT: H 350 MET cc_start: 0.8390 (ttt) cc_final: 0.8034 (ttt) REVERT: H 444 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8659 (tt) REVERT: H 489 MET cc_start: 0.6034 (mtp) cc_final: 0.5636 (mtm) REVERT: I 158 LEU cc_start: 0.7576 (mp) cc_final: 0.7269 (mt) REVERT: I 222 MET cc_start: 0.5111 (ptp) cc_final: 0.2542 (tpp) REVERT: J 480 ASN cc_start: 0.7748 (m-40) cc_final: 0.7328 (m-40) REVERT: K 136 GLN cc_start: 0.4086 (OUTLIER) cc_final: 0.3771 (mp10) REVERT: K 155 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5552 (mm-30) REVERT: K 193 TYR cc_start: 0.6137 (t80) cc_final: 0.5793 (t80) REVERT: L 128 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8471 (pp) REVERT: L 216 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6338 (tm-30) REVERT: N 94 LYS cc_start: 0.6716 (pttm) cc_final: 0.6009 (ptpp) REVERT: O 51 GLU cc_start: 0.6345 (mt-10) cc_final: 0.6098 (mm-30) outliers start: 74 outliers final: 56 residues processed: 494 average time/residue: 0.3598 time to fit residues: 272.5105 Evaluate side-chains 509 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 446 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain G residue 86 ASN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 396 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 213 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 122 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 0.6980 chunk 245 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 272 optimal weight: 0.2980 chunk 226 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22887 Z= 0.159 Angle : 0.521 6.865 30929 Z= 0.270 Chirality : 0.040 0.173 3443 Planarity : 0.004 0.053 4017 Dihedral : 4.665 50.699 3159 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.55 % Allowed : 15.95 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 2860 helix: 1.85 (0.13), residues: 1560 sheet: 0.12 (0.35), residues: 224 loop : -1.16 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 151 HIS 0.018 0.001 HIS H 484 PHE 0.014 0.001 PHE J 371 TYR 0.018 0.001 TYR E 154 ARG 0.008 0.000 ARG N 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 476 time to evaluate : 2.466 Fit side-chains REVERT: A 21 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7161 (mm) REVERT: A 164 ARG cc_start: 0.8418 (mpt180) cc_final: 0.8039 (mmm-85) REVERT: B 156 HIS cc_start: 0.7868 (p-80) cc_final: 0.7667 (p-80) REVERT: B 170 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: B 176 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8697 (tp) REVERT: B 215 GLU cc_start: 0.6600 (mt-10) cc_final: 0.5568 (mt-10) REVERT: D 51 GLN cc_start: 0.5408 (mp-120) cc_final: 0.5107 (mp10) REVERT: D 96 TYR cc_start: 0.7189 (t80) cc_final: 0.6771 (t80) REVERT: D 118 ARG cc_start: 0.7329 (mtm-85) cc_final: 0.6745 (mtt90) REVERT: E 161 LYS cc_start: 0.7364 (ptmt) cc_final: 0.6549 (mttt) REVERT: G 43 SER cc_start: 0.7240 (t) cc_final: 0.7018 (p) REVERT: G 101 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8590 (tp) REVERT: G 151 MET cc_start: 0.7163 (mtp) cc_final: 0.6461 (mtp) REVERT: H 350 MET cc_start: 0.8348 (ttt) cc_final: 0.8098 (ttt) REVERT: H 489 MET cc_start: 0.5819 (mtp) cc_final: 0.5475 (mtm) REVERT: I 158 LEU cc_start: 0.7359 (mp) cc_final: 0.7054 (mt) REVERT: I 222 MET cc_start: 0.4982 (ptp) cc_final: 0.2512 (tpp) REVERT: J 480 ASN cc_start: 0.7724 (m-40) cc_final: 0.7325 (m-40) REVERT: K 152 ILE cc_start: 0.6407 (OUTLIER) cc_final: 0.6076 (tp) REVERT: K 155 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5656 (mm-30) REVERT: K 193 TYR cc_start: 0.6079 (t80) cc_final: 0.5835 (t80) REVERT: L 128 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8458 (pp) REVERT: N 94 LYS cc_start: 0.6477 (pttm) cc_final: 0.5887 (ptpp) REVERT: N 164 MET cc_start: 0.8049 (mmm) cc_final: 0.7687 (mtt) REVERT: O 51 GLU cc_start: 0.6335 (mt-10) cc_final: 0.5389 (mt-10) outliers start: 61 outliers final: 37 residues processed: 510 average time/residue: 0.3587 time to fit residues: 280.6188 Evaluate side-chains 494 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 450 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 350 MET Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 213 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 0.0040 chunk 30 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 271 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN D 56 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 GLN L 61 GLN L 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22887 Z= 0.239 Angle : 0.551 7.203 30929 Z= 0.284 Chirality : 0.042 0.240 3443 Planarity : 0.004 0.053 4017 Dihedral : 4.684 51.696 3158 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.17 % Allowed : 15.91 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2860 helix: 1.84 (0.13), residues: 1558 sheet: 0.07 (0.35), residues: 234 loop : -1.16 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 151 HIS 0.010 0.001 HIS H 484 PHE 0.011 0.001 PHE J 371 TYR 0.023 0.002 TYR C 154 ARG 0.007 0.000 ARG G 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 454 time to evaluate : 2.655 Fit side-chains REVERT: A 164 ARG cc_start: 0.8443 (mpt180) cc_final: 0.8050 (mmm-85) REVERT: A 199 ASP cc_start: 0.8016 (m-30) cc_final: 0.7708 (m-30) REVERT: B 170 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: B 215 GLU cc_start: 0.6603 (mt-10) cc_final: 0.5564 (mt-10) REVERT: D 96 TYR cc_start: 0.7204 (t80) cc_final: 0.6789 (t80) REVERT: D 118 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.6769 (mtt90) REVERT: E 161 LYS cc_start: 0.7365 (ptmt) cc_final: 0.6574 (mttt) REVERT: G 101 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8635 (tp) REVERT: G 151 MET cc_start: 0.7207 (mtp) cc_final: 0.6524 (mtp) REVERT: H 350 MET cc_start: 0.8364 (ttt) cc_final: 0.8100 (ttt) REVERT: H 444 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8646 (tt) REVERT: H 489 MET cc_start: 0.5793 (mtp) cc_final: 0.5416 (mtm) REVERT: I 158 LEU cc_start: 0.7527 (mp) cc_final: 0.7235 (mt) REVERT: I 222 MET cc_start: 0.5046 (ptp) cc_final: 0.2500 (tpp) REVERT: J 480 ASN cc_start: 0.7786 (m-40) cc_final: 0.7391 (m-40) REVERT: K 136 GLN cc_start: 0.4051 (OUTLIER) cc_final: 0.3764 (mp10) REVERT: K 152 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.6219 (tp) REVERT: K 155 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.5583 (mm-30) REVERT: K 193 TYR cc_start: 0.6106 (t80) cc_final: 0.5869 (t80) REVERT: L 128 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8451 (pp) REVERT: M 417 LEU cc_start: 0.7160 (mt) cc_final: 0.6777 (mt) REVERT: N 94 LYS cc_start: 0.6466 (pttm) cc_final: 0.5880 (ptpp) REVERT: N 164 MET cc_start: 0.8071 (mmm) cc_final: 0.7783 (mtt) outliers start: 76 outliers final: 57 residues processed: 497 average time/residue: 0.3728 time to fit residues: 283.7650 Evaluate side-chains 514 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 450 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 350 MET Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain J residue 491 ASN Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 213 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 122 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22887 Z= 0.174 Angle : 0.530 7.271 30929 Z= 0.273 Chirality : 0.041 0.188 3443 Planarity : 0.004 0.053 4017 Dihedral : 4.601 50.881 3158 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.38 % Allowed : 16.08 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2860 helix: 1.97 (0.13), residues: 1559 sheet: 0.15 (0.34), residues: 241 loop : -1.08 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 151 HIS 0.008 0.001 HIS H 484 PHE 0.010 0.001 PHE E 90 TYR 0.029 0.001 TYR L 196 ARG 0.006 0.000 ARG G 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 465 time to evaluate : 2.684 Fit side-chains REVERT: A 164 ARG cc_start: 0.8403 (mpt180) cc_final: 0.8046 (mmm-85) REVERT: B 170 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: B 215 GLU cc_start: 0.6571 (mt-10) cc_final: 0.5529 (mt-10) REVERT: D 96 TYR cc_start: 0.7211 (t80) cc_final: 0.6796 (t80) REVERT: D 118 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.6765 (mtt90) REVERT: E 112 MET cc_start: 0.7546 (mmp) cc_final: 0.7309 (mmp) REVERT: E 161 LYS cc_start: 0.7376 (ptmt) cc_final: 0.6782 (mttt) REVERT: F 115 ARG cc_start: 0.7112 (mmm-85) cc_final: 0.6753 (mtp85) REVERT: G 101 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8603 (tp) REVERT: G 147 LEU cc_start: 0.7360 (mt) cc_final: 0.7039 (mp) REVERT: G 151 MET cc_start: 0.7172 (mtp) cc_final: 0.6512 (mtp) REVERT: H 350 MET cc_start: 0.8321 (ttt) cc_final: 0.7993 (ttt) REVERT: H 444 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8625 (tt) REVERT: H 489 MET cc_start: 0.5706 (mtp) cc_final: 0.5341 (mtt) REVERT: I 38 ILE cc_start: 0.8736 (mt) cc_final: 0.8478 (mt) REVERT: I 158 LEU cc_start: 0.7357 (mp) cc_final: 0.7019 (mt) REVERT: I 222 MET cc_start: 0.4660 (ptp) cc_final: 0.2315 (tpp) REVERT: J 480 ASN cc_start: 0.7773 (m-40) cc_final: 0.7351 (m-40) REVERT: K 136 GLN cc_start: 0.4034 (OUTLIER) cc_final: 0.3754 (mp10) REVERT: K 152 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6155 (tp) REVERT: K 155 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5745 (mm-30) REVERT: K 193 TYR cc_start: 0.6088 (t80) cc_final: 0.5845 (t80) REVERT: L 128 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8430 (pp) REVERT: N 94 LYS cc_start: 0.6450 (pttm) cc_final: 0.5886 (ptpp) REVERT: N 164 MET cc_start: 0.8038 (mmm) cc_final: 0.7772 (mtt) REVERT: O 118 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.4943 (tmm) outliers start: 81 outliers final: 56 residues processed: 505 average time/residue: 0.3673 time to fit residues: 282.1244 Evaluate side-chains 518 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 454 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain J residue 350 MET Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 213 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 122 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 101 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22887 Z= 0.191 Angle : 0.538 7.218 30929 Z= 0.276 Chirality : 0.041 0.280 3443 Planarity : 0.004 0.053 4017 Dihedral : 4.583 50.892 3158 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.22 % Allowed : 16.16 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 2860 helix: 1.98 (0.13), residues: 1559 sheet: 0.21 (0.34), residues: 241 loop : -1.04 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 151 HIS 0.007 0.001 HIS H 484 PHE 0.011 0.001 PHE I 102 TYR 0.026 0.001 TYR L 196 ARG 0.008 0.000 ARG G 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 458 time to evaluate : 2.487 Fit side-chains REVERT: A 164 ARG cc_start: 0.8402 (mpt180) cc_final: 0.8053 (mmm-85) REVERT: B 170 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: B 215 GLU cc_start: 0.6607 (mt-10) cc_final: 0.5573 (mt-10) REVERT: C 72 MET cc_start: 0.8593 (mmm) cc_final: 0.8029 (mmm) REVERT: D 96 TYR cc_start: 0.7154 (t80) cc_final: 0.6737 (t80) REVERT: D 118 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.6873 (mtt90) REVERT: D 200 LYS cc_start: 0.8632 (ttpt) cc_final: 0.8344 (ttpp) REVERT: E 112 MET cc_start: 0.7542 (mmp) cc_final: 0.7274 (mmt) REVERT: E 161 LYS cc_start: 0.7372 (ptmt) cc_final: 0.6789 (mttt) REVERT: F 115 ARG cc_start: 0.7057 (mmm-85) cc_final: 0.6751 (mtp85) REVERT: G 101 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8613 (tp) REVERT: G 147 LEU cc_start: 0.7365 (mt) cc_final: 0.7065 (mp) REVERT: G 151 MET cc_start: 0.7171 (mtp) cc_final: 0.6507 (mtp) REVERT: H 350 MET cc_start: 0.8321 (ttt) cc_final: 0.8030 (ttt) REVERT: H 444 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8642 (tt) REVERT: I 158 LEU cc_start: 0.7483 (mp) cc_final: 0.7218 (mt) REVERT: I 222 MET cc_start: 0.4687 (ptp) cc_final: 0.2345 (tpp) REVERT: J 480 ASN cc_start: 0.7787 (m-40) cc_final: 0.7356 (m-40) REVERT: K 136 GLN cc_start: 0.4022 (OUTLIER) cc_final: 0.3747 (mp10) REVERT: K 149 TYR cc_start: 0.6359 (t80) cc_final: 0.6075 (t80) REVERT: K 152 ILE cc_start: 0.6465 (OUTLIER) cc_final: 0.6165 (tp) REVERT: K 155 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5709 (mm-30) REVERT: K 193 TYR cc_start: 0.6093 (t80) cc_final: 0.5860 (t80) REVERT: K 208 VAL cc_start: 0.6979 (m) cc_final: 0.6716 (m) REVERT: L 128 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8439 (pp) REVERT: M 355 PHE cc_start: 0.7291 (p90) cc_final: 0.7016 (p90) REVERT: N 94 LYS cc_start: 0.6387 (pttm) cc_final: 0.5859 (ptpp) REVERT: N 164 MET cc_start: 0.8032 (mmm) cc_final: 0.7772 (mtt) REVERT: O 73 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7090 (mt-10) REVERT: O 118 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.5041 (tmm) outliers start: 77 outliers final: 60 residues processed: 500 average time/residue: 0.3603 time to fit residues: 274.3376 Evaluate side-chains 518 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 450 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain J residue 350 MET Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 407 HIS Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 213 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 122 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 7.9990 chunk 267 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 492 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN L 206 ASN N 204 ASN N 252 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 22887 Z= 0.392 Angle : 0.658 7.296 30929 Z= 0.338 Chirality : 0.046 0.261 3443 Planarity : 0.005 0.052 4017 Dihedral : 4.994 52.223 3158 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.13 % Allowed : 16.45 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2860 helix: 1.61 (0.13), residues: 1548 sheet: -0.19 (0.33), residues: 251 loop : -1.21 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 11 HIS 0.010 0.001 HIS J 407 PHE 0.015 0.002 PHE M 371 TYR 0.039 0.002 TYR K 85 ARG 0.006 0.001 ARG G 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 453 time to evaluate : 2.405 Fit side-chains REVERT: A 164 ARG cc_start: 0.8377 (mpt180) cc_final: 0.7985 (mmm-85) REVERT: A 199 ASP cc_start: 0.8130 (m-30) cc_final: 0.7780 (m-30) REVERT: B 170 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: B 215 GLU cc_start: 0.6709 (mt-10) cc_final: 0.5650 (mt-10) REVERT: C 44 GLN cc_start: 0.7994 (mt0) cc_final: 0.7788 (mt0) REVERT: D 96 TYR cc_start: 0.7169 (t80) cc_final: 0.6732 (t80) REVERT: D 118 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.6655 (mtt90) REVERT: D 200 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8387 (ttpp) REVERT: E 112 MET cc_start: 0.7584 (mmp) cc_final: 0.7308 (mmt) REVERT: E 161 LYS cc_start: 0.7242 (ptmt) cc_final: 0.6653 (mttt) REVERT: F 115 ARG cc_start: 0.7139 (mmm-85) cc_final: 0.6835 (mtp85) REVERT: G 101 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8677 (tp) REVERT: G 151 MET cc_start: 0.7147 (mtp) cc_final: 0.6457 (mtp) REVERT: H 350 MET cc_start: 0.8297 (ttt) cc_final: 0.7985 (ttt) REVERT: H 444 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8581 (tt) REVERT: H 489 MET cc_start: 0.5969 (mtp) cc_final: 0.5651 (mtm) REVERT: I 222 MET cc_start: 0.4828 (ptp) cc_final: 0.2336 (tpp) REVERT: J 480 ASN cc_start: 0.7829 (m-40) cc_final: 0.7391 (m-40) REVERT: K 136 GLN cc_start: 0.4286 (OUTLIER) cc_final: 0.4029 (mp10) REVERT: K 152 ILE cc_start: 0.6535 (OUTLIER) cc_final: 0.6216 (tp) REVERT: K 155 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5811 (mm-30) REVERT: K 208 VAL cc_start: 0.7209 (m) cc_final: 0.6939 (m) REVERT: L 128 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8435 (pp) REVERT: M 414 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7303 (mm-30) REVERT: O 73 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7207 (mt-10) REVERT: O 118 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5209 (tmm) outliers start: 75 outliers final: 60 residues processed: 496 average time/residue: 0.3676 time to fit residues: 277.4564 Evaluate side-chains 512 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 444 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain H residue 396 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 443 SER Chi-restraints excluded: chain H residue 444 LEU Chi-restraints excluded: chain H residue 464 THR Chi-restraints excluded: chain H residue 477 ILE Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain J residue 350 MET Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 464 THR Chi-restraints excluded: chain K residue 136 GLN Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 171 THR Chi-restraints excluded: chain K residue 179 PHE Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain L residue 128 LEU Chi-restraints excluded: chain M residue 460 ASP Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain N residue 213 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 118 MET Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 0.9990 chunk 238 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 101 GLN B 60 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 492 GLN ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN L 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.159732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130683 restraints weight = 26817.598| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.60 r_work: 0.3296 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22887 Z= 0.186 Angle : 0.552 7.508 30929 Z= 0.283 Chirality : 0.041 0.163 3443 Planarity : 0.004 0.054 4017 Dihedral : 4.744 49.694 3158 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.96 % Allowed : 16.91 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2860 helix: 1.84 (0.13), residues: 1560 sheet: 0.06 (0.34), residues: 236 loop : -1.09 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 11 HIS 0.016 0.001 HIS J 407 PHE 0.011 0.001 PHE J 371 TYR 0.032 0.001 TYR K 85 ARG 0.008 0.000 ARG G 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5757.03 seconds wall clock time: 105 minutes 41.24 seconds (6341.24 seconds total)