Starting phenix.real_space_refine on Sun Mar 24 00:41:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9b_27962/03_2024/8e9b_27962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9b_27962/03_2024/8e9b_27962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9b_27962/03_2024/8e9b_27962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9b_27962/03_2024/8e9b_27962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9b_27962/03_2024/8e9b_27962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9b_27962/03_2024/8e9b_27962_updated.pdb" } resolution = 3.5 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= 0.004 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: 6 Type Number sf(0) Gaussians P 21 5.49 5 Mg 10 5.21 5 S 230 5.16 5 C 24757 2.51 5 N 6659 2.21 5 O 7483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M GLU 226": "OE1" <-> "OE2" Residue "M GLU 259": "OE1" <-> "OE2" Residue "M GLU 270": "OE1" <-> "OE2" Residue "N GLU 72": "OE1" <-> "OE2" Residue "N GLU 93": "OE1" <-> "OE2" Residue "N GLU 99": "OE1" <-> "OE2" Residue "N GLU 125": "OE1" <-> "OE2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "N GLU 205": "OE1" <-> "OE2" Residue "N GLU 224": "OE1" <-> "OE2" Residue "N GLU 237": "OE1" <-> "OE2" Residue "N GLU 253": "OE1" <-> "OE2" Residue "N ARG 254": "NH1" <-> "NH2" Residue "N GLU 259": "OE1" <-> "OE2" Residue "N GLU 316": "OE1" <-> "OE2" Residue "N GLU 334": "OE1" <-> "OE2" Residue "N ASP 363": "OD1" <-> "OD2" Residue "O GLU 93": "OE1" <-> "OE2" Residue "O GLU 205": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O GLU 214": "OE1" <-> "OE2" Residue "O GLU 226": "OE1" <-> "OE2" Residue "O GLU 253": "OE1" <-> "OE2" Residue "O PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 334": "OE1" <-> "OE2" Residue "O GLU 364": "OE1" <-> "OE2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "P GLU 93": "OE1" <-> "OE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "P GLU 125": "OE1" <-> "OE2" Residue "P GLU 214": "OE1" <-> "OE2" Residue "P GLU 237": "OE1" <-> "OE2" Residue "P PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 316": "OE1" <-> "OE2" Residue "Q GLU 117": "OE1" <-> "OE2" Residue "Q GLU 214": "OE1" <-> "OE2" Residue "Q GLU 316": "OE1" <-> "OE2" Residue "Q GLU 334": "OE1" <-> "OE2" Residue "Q GLU 364": "OE1" <-> "OE2" Residue "R GLU 57": "OE1" <-> "OE2" Residue "R GLU 214": "OE1" <-> "OE2" Residue "R GLU 361": "OE1" <-> "OE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "H GLU 224": "OE1" <-> "OE2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H GLU 276": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "I GLU 205": "OE1" <-> "OE2" Residue "I GLU 207": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39160 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3156 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 1 Chain: "B" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3089 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 19, 'TRANS': 367} Chain: "C" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2825 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2584 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 301} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1390 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 161} Chain: "F" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1377 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "G" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1183 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "M" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.86, per 1000 atoms: 0.51 Number of scatterers: 39160 At special positions: 0 Unit cell: (222.332, 218.24, 129.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 230 16.00 P 21 15.00 Mg 10 11.99 O 7483 8.00 N 6659 7.00 C 24757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 217 " - pdb=" SG CYS N 257 " distance=2.82 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: 16.84 Conformation dependent library (CDL) restraints added in 6.9 seconds 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 222 helices and 59 sheets defined 40.9% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.52 Creating SS restraints... Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 320 through 328 removed outlier: 4.525A pdb=" N LYS A 324 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 328 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 342 through 365 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'B' and resid 56 through 64 removed outlier: 5.920A pdb=" N SER B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.595A pdb=" N TYR B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.051A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 253 through 262 Proline residue: B 258 - end of helix removed outlier: 5.207A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.760A pdb=" N ARG B 290 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 324 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 349 through 360 removed outlier: 3.786A pdb=" N ASP B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 371 through 377 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 68 through 78 removed outlier: 7.892A pdb=" N ALA D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 114 through 139 removed outlier: 4.833A pdb=" N ALA D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 141 through 154 Proline residue: D 145 - end of helix removed outlier: 3.766A pdb=" N GLN D 154 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 205 removed outlier: 4.039A pdb=" N VAL D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 255 through 295 removed outlier: 5.398A pdb=" N ARG D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 56 removed outlier: 4.291A pdb=" N ARG E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 83 Processing helix chain 'E' and resid 90 through 100 Processing helix chain 'E' and resid 124 through 149 Processing helix chain 'E' and resid 159 through 162 No H-bonds generated for 'chain 'E' and resid 159 through 162' Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'F' and resid 6 through 18 Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 81 through 100 removed outlier: 3.774A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU F 99 " --> pdb=" O MET F 95 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N SER F 100 " --> pdb=" O GLY F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 131 through 167 removed outlier: 4.523A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS F 167 " --> pdb=" O THR F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 12 No H-bonds generated for 'chain 'G' and resid 9 through 12' Processing helix chain 'G' and resid 18 through 20 No H-bonds generated for 'chain 'G' and resid 18 through 20' Processing helix chain 'G' and resid 29 through 48 Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 70 through 85 Processing helix chain 'G' and resid 89 through 97 Proline residue: G 93 - end of helix Processing helix chain 'G' and resid 101 through 116 Processing helix chain 'G' and resid 123 through 136 Processing helix chain 'G' and resid 140 through 146 Processing helix chain 'M' and resid 55 through 64 removed outlier: 5.699A pdb=" N GLY M 63 " --> pdb=" O GLN M 59 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 91 Processing helix chain 'M' and resid 98 through 100 No H-bonds generated for 'chain 'M' and resid 98 through 100' Processing helix chain 'M' and resid 113 through 125 Processing helix chain 'M' and resid 137 through 145 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 182 through 196 removed outlier: 3.815A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG M 196 " --> pdb=" O ILE M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 216 Processing helix chain 'M' and resid 223 through 232 removed outlier: 4.097A pdb=" N SER M 232 " --> pdb=" O ALA M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 256 removed outlier: 3.801A pdb=" N ARG M 256 " --> pdb=" O GLU M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 261 Processing helix chain 'M' and resid 264 through 267 Processing helix chain 'M' and resid 274 through 284 Processing helix chain 'M' and resid 290 through 295 Processing helix chain 'M' and resid 302 through 305 Processing helix chain 'M' and resid 309 through 320 Processing helix chain 'M' and resid 338 through 348 Processing helix chain 'M' and resid 350 through 352 No H-bonds generated for 'chain 'M' and resid 350 through 352' Processing helix chain 'M' and resid 359 through 365 removed outlier: 4.387A pdb=" N GLU M 364 " --> pdb=" O GLN M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 374 removed outlier: 3.545A pdb=" N HIS M 371 " --> pdb=" O SER M 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS M 374 " --> pdb=" O HIS M 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 64 removed outlier: 5.849A pdb=" N GLY N 63 " --> pdb=" O GLN N 59 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 91 Processing helix chain 'N' and resid 98 through 100 No H-bonds generated for 'chain 'N' and resid 98 through 100' Processing helix chain 'N' and resid 113 through 125 Processing helix chain 'N' and resid 137 through 145 Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 182 through 196 removed outlier: 4.055A pdb=" N GLU N 195 " --> pdb=" O LYS N 191 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG N 196 " --> pdb=" O ILE N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 216 Processing helix chain 'N' and resid 223 through 231 Processing helix chain 'N' and resid 252 through 256 removed outlier: 3.735A pdb=" N ARG N 256 " --> pdb=" O GLU N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 264 through 267 Processing helix chain 'N' and resid 274 through 283 removed outlier: 3.699A pdb=" N THR N 278 " --> pdb=" O ILE N 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR N 279 " --> pdb=" O HIS N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 295 removed outlier: 4.097A pdb=" N LYS N 291 " --> pdb=" O ASP N 288 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP N 292 " --> pdb=" O ILE N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 303 through 305 No H-bonds generated for 'chain 'N' and resid 303 through 305' Processing helix chain 'N' and resid 309 through 320 removed outlier: 3.525A pdb=" N MET N 313 " --> pdb=" O ILE N 309 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN N 314 " --> pdb=" O ALA N 310 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR N 318 " --> pdb=" O GLN N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 347 removed outlier: 5.245A pdb=" N VAL N 339 " --> pdb=" O LYS N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 365 removed outlier: 4.434A pdb=" N GLU N 364 " --> pdb=" O GLN N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 373 Processing helix chain 'O' and resid 56 through 60 Processing helix chain 'O' and resid 62 through 64 No H-bonds generated for 'chain 'O' and resid 62 through 64' Processing helix chain 'O' and resid 79 through 91 Processing helix chain 'O' and resid 98 through 100 No H-bonds generated for 'chain 'O' and resid 98 through 100' Processing helix chain 'O' and resid 113 through 125 Processing helix chain 'O' and resid 137 through 145 Processing helix chain 'O' and resid 182 through 196 removed outlier: 3.584A pdb=" N THR O 194 " --> pdb=" O MET O 190 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 215 removed outlier: 3.741A pdb=" N LYS O 215 " --> pdb=" O ASP O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 224 through 229 Processing helix chain 'O' and resid 252 through 261 removed outlier: 3.753A pdb=" N ARG O 256 " --> pdb=" O GLU O 253 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N CYS O 257 " --> pdb=" O ARG O 254 " (cutoff:3.500A) Proline residue: O 258 - end of helix Processing helix chain 'O' and resid 264 through 267 Processing helix chain 'O' and resid 274 through 284 removed outlier: 3.757A pdb=" N TYR O 279 " --> pdb=" O HIS O 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 294 Processing helix chain 'O' and resid 303 through 305 No H-bonds generated for 'chain 'O' and resid 303 through 305' Processing helix chain 'O' and resid 309 through 320 Processing helix chain 'O' and resid 335 through 347 removed outlier: 3.512A pdb=" N SER O 338 " --> pdb=" O ARG O 335 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL O 339 " --> pdb=" O LYS O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 350 through 355 removed outlier: 3.674A pdb=" N GLN O 353 " --> pdb=" O SER O 350 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN O 354 " --> pdb=" O THR O 351 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 365 Processing helix chain 'O' and resid 367 through 373 removed outlier: 3.837A pdb=" N VAL O 370 " --> pdb=" O PRO O 367 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS O 373 " --> pdb=" O VAL O 370 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 64 removed outlier: 6.186A pdb=" N GLY P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 91 Processing helix chain 'P' and resid 113 through 125 Processing helix chain 'P' and resid 137 through 145 Processing helix chain 'P' and resid 182 through 196 removed outlier: 3.812A pdb=" N THR P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU P 195 " --> pdb=" O LYS P 191 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG P 196 " --> pdb=" O ILE P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 215 removed outlier: 3.521A pdb=" N LYS P 215 " --> pdb=" O ASP P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 224 through 231 removed outlier: 3.936A pdb=" N ALA P 231 " --> pdb=" O MET P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 256 removed outlier: 3.719A pdb=" N ARG P 256 " --> pdb=" O GLU P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 261 Processing helix chain 'P' and resid 264 through 267 removed outlier: 3.545A pdb=" N ILE P 267 " --> pdb=" O PRO P 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 264 through 267' Processing helix chain 'P' and resid 274 through 283 Processing helix chain 'P' and resid 290 through 295 Processing helix chain 'P' and resid 302 through 305 Processing helix chain 'P' and resid 309 through 320 Processing helix chain 'P' and resid 335 through 347 removed outlier: 5.136A pdb=" N VAL P 339 " --> pdb=" O LYS P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 352 through 355 Processing helix chain 'P' and resid 359 through 373 removed outlier: 3.807A pdb=" N GLU P 364 " --> pdb=" O GLN P 360 " (cutoff:3.500A) Proline residue: P 367 - end of helix removed outlier: 5.634A pdb=" N VAL P 370 " --> pdb=" O GLY P 366 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N HIS P 371 " --> pdb=" O PRO P 367 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG P 372 " --> pdb=" O SER P 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 60 Processing helix chain 'Q' and resid 62 through 64 No H-bonds generated for 'chain 'Q' and resid 62 through 64' Processing helix chain 'Q' and resid 79 through 91 Processing helix chain 'Q' and resid 98 through 100 No H-bonds generated for 'chain 'Q' and resid 98 through 100' Processing helix chain 'Q' and resid 113 through 125 Processing helix chain 'Q' and resid 137 through 145 Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 182 through 192 Processing helix chain 'Q' and resid 194 through 196 No H-bonds generated for 'chain 'Q' and resid 194 through 196' Processing helix chain 'Q' and resid 203 through 216 Processing helix chain 'Q' and resid 223 through 231 Processing helix chain 'Q' and resid 252 through 260 removed outlier: 3.732A pdb=" N ARG Q 256 " --> pdb=" O GLU Q 253 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N CYS Q 257 " --> pdb=" O ARG Q 254 " (cutoff:3.500A) Proline residue: Q 258 - end of helix Processing helix chain 'Q' and resid 264 through 267 Processing helix chain 'Q' and resid 276 through 283 Processing helix chain 'Q' and resid 287 through 293 removed outlier: 4.258A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 303 through 305 No H-bonds generated for 'chain 'Q' and resid 303 through 305' Processing helix chain 'Q' and resid 309 through 320 Processing helix chain 'Q' and resid 335 through 347 removed outlier: 5.249A pdb=" N VAL Q 339 " --> pdb=" O LYS Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 350 through 355 removed outlier: 4.327A pdb=" N GLN Q 354 " --> pdb=" O THR Q 351 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 362 No H-bonds generated for 'chain 'Q' and resid 359 through 362' Processing helix chain 'Q' and resid 367 through 373 removed outlier: 3.691A pdb=" N VAL Q 370 " --> pdb=" O PRO Q 367 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS Q 373 " --> pdb=" O VAL Q 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 60 Processing helix chain 'R' and resid 79 through 91 Processing helix chain 'R' and resid 113 through 125 Processing helix chain 'R' and resid 139 through 145 Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 182 through 193 Processing helix chain 'R' and resid 203 through 215 Processing helix chain 'R' and resid 223 through 232 removed outlier: 3.800A pdb=" N SER R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 256 removed outlier: 3.753A pdb=" N ARG R 256 " --> pdb=" O GLU R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 260 No H-bonds generated for 'chain 'R' and resid 258 through 260' Processing helix chain 'R' and resid 264 through 267 Processing helix chain 'R' and resid 274 through 284 Processing helix chain 'R' and resid 287 through 295 removed outlier: 5.119A pdb=" N LYS R 291 " --> pdb=" O ASP R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 305 No H-bonds generated for 'chain 'R' and resid 303 through 305' Processing helix chain 'R' and resid 309 through 320 Processing helix chain 'R' and resid 335 through 348 removed outlier: 3.661A pdb=" N SER R 338 " --> pdb=" O ARG R 335 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL R 339 " --> pdb=" O LYS R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 352 through 355 Processing helix chain 'R' and resid 359 through 373 removed outlier: 3.779A pdb=" N GLU R 364 " --> pdb=" O GLN R 360 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA R 365 " --> pdb=" O GLU R 361 " (cutoff:3.500A) Proline residue: R 367 - end of helix removed outlier: 5.125A pdb=" N VAL R 370 " --> pdb=" O GLY R 366 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N HIS R 371 " --> pdb=" O PRO R 367 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS R 373 " --> pdb=" O ILE R 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 79 through 92 Processing helix chain 'H' and resid 113 through 127 Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.905A pdb=" N SER H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 182 through 196 removed outlier: 3.665A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 215 Processing helix chain 'H' and resid 223 through 231 removed outlier: 3.833A pdb=" N ALA H 231 " --> pdb=" O MET H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.718A pdb=" N ARG H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 261 Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 284 Processing helix chain 'H' and resid 287 through 293 removed outlier: 4.151A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 305 No H-bonds generated for 'chain 'H' and resid 303 through 305' Processing helix chain 'H' and resid 309 through 320 Processing helix chain 'H' and resid 338 through 348 Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.979A pdb=" N GLN H 353 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET H 355 " --> pdb=" O PHE H 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 350 through 355' Processing helix chain 'H' and resid 359 through 363 Processing helix chain 'H' and resid 367 through 373 removed outlier: 4.030A pdb=" N LYS H 373 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 137 through 144 Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 182 through 196 removed outlier: 4.852A pdb=" N GLU I 195 " --> pdb=" O LYS I 191 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 215 removed outlier: 3.584A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP I 211 " --> pdb=" O GLU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 231 removed outlier: 3.926A pdb=" N ALA I 231 " --> pdb=" O MET I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 262 removed outlier: 3.535A pdb=" N ARG I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N CYS I 257 " --> pdb=" O ARG I 254 " (cutoff:3.500A) Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 264 through 267 Processing helix chain 'I' and resid 276 through 284 Processing helix chain 'I' and resid 287 through 295 removed outlier: 4.596A pdb=" N LYS I 291 " --> pdb=" O ASP I 288 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP I 292 " --> pdb=" O ILE I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 305 No H-bonds generated for 'chain 'I' and resid 303 through 305' Processing helix chain 'I' and resid 309 through 320 Processing helix chain 'I' and resid 338 through 347 Processing helix chain 'I' and resid 352 through 354 No H-bonds generated for 'chain 'I' and resid 352 through 354' Processing helix chain 'I' and resid 359 through 362 No H-bonds generated for 'chain 'I' and resid 359 through 362' Processing helix chain 'I' and resid 367 through 373 removed outlier: 3.616A pdb=" N HIS I 371 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS I 373 " --> pdb=" O VAL I 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 16 through 19 removed outlier: 4.113A pdb=" N TYR A 29 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 74 through 76 Processing sheet with id= C, first strand: chain 'A' and resid 125 through 130 removed outlier: 6.432A pdb=" N GLY A 154 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU A 128 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR A 156 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLU A 130 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA A 158 " --> pdb=" O GLU A 130 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 330 through 333 removed outlier: 6.329A pdb=" N THR A 182 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER A 333 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 207 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 267 through 269 Processing sheet with id= F, first strand: chain 'B' and resid 6 through 10 removed outlier: 3.624A pdb=" N PHE B 27 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= H, first strand: chain 'B' and resid 102 through 107 removed outlier: 6.306A pdb=" N GLY B 131 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU B 105 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR B 133 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLU B 107 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA B 135 " --> pdb=" O GLU B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 160 through 165 Processing sheet with id= J, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.565A pdb=" N TYR B 240 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 17 through 19 removed outlier: 3.738A pdb=" N ARG C 49 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU C 39 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N HIS C 47 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP C 41 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 79 through 83 Processing sheet with id= N, first strand: chain 'C' and resid 135 through 140 removed outlier: 3.613A pdb=" N VAL C 137 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR C 128 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE C 105 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 149 through 154 removed outlier: 6.500A pdb=" N GLY C 164 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU C 152 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA C 162 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N TRP C 154 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C 160 " --> pdb=" O TRP C 154 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS C 165 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER C 174 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL C 198 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 210 through 213 removed outlier: 3.998A pdb=" N ALA C 210 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA C 243 " --> pdb=" O TYR C 233 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 254 through 259 removed outlier: 6.687A pdb=" N ALA C 268 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 257 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 266 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TRP C 259 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA C 264 " --> pdb=" O TRP C 259 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 276 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLN C 278 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N HIS C 286 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASN C 280 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TRP C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.728A pdb=" N SER C 366 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU C 350 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 364 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 28 through 32 removed outlier: 3.566A pdb=" N PHE D 88 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 157 through 159 removed outlier: 3.534A pdb=" N LEU D 245 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 214 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 114 through 118 removed outlier: 4.104A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN F 56 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N CYS F 61 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N SER F 54 " --> pdb=" O CYS F 61 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE F 63 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL F 52 " --> pdb=" O ILE F 63 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 8 through 11 removed outlier: 3.598A pdb=" N PHE M 31 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA M 29 " --> pdb=" O ALA M 19 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 34 through 38 Processing sheet with id= X, first strand: chain 'M' and resid 105 through 107 removed outlier: 3.580A pdb=" N GLU M 107 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 298 through 300 Processing sheet with id= Z, first strand: chain 'M' and resid 238 through 241 Processing sheet with id= AA, first strand: chain 'N' and resid 8 through 10 removed outlier: 3.938A pdb=" N THR N 106 " --> pdb=" O CYS N 10 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 16 through 19 removed outlier: 3.537A pdb=" N PHE N 31 " --> pdb=" O VAL N 17 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 52 through 54 removed outlier: 3.542A pdb=" N VAL N 35 " --> pdb=" O LYS N 68 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 153 through 155 Processing sheet with id= AE, first strand: chain 'N' and resid 238 through 241 removed outlier: 3.881A pdb=" N ILE N 250 " --> pdb=" O LYS N 238 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'O' and resid 8 through 12 Processing sheet with id= AG, first strand: chain 'O' and resid 35 through 38 removed outlier: 3.560A pdb=" N VAL O 35 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG O 37 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'O' and resid 103 through 107 Processing sheet with id= AI, first strand: chain 'O' and resid 297 through 299 removed outlier: 6.896A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL O 152 " --> pdb=" O VAL O 163 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 238 through 241 removed outlier: 3.895A pdb=" N LYS O 238 " --> pdb=" O ILE O 250 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE O 250 " --> pdb=" O LYS O 238 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 8 through 11 Processing sheet with id= AL, first strand: chain 'P' and resid 105 through 107 removed outlier: 3.515A pdb=" N GLU P 107 " --> pdb=" O ALA P 135 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'P' and resid 297 through 300 removed outlier: 6.776A pdb=" N ILE P 151 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER P 300 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU P 153 " --> pdb=" O SER P 300 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 238 through 241 Processing sheet with id= AO, first strand: chain 'Q' and resid 8 through 12 removed outlier: 3.628A pdb=" N PHE Q 31 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA Q 29 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Q' and resid 52 through 54 Processing sheet with id= AQ, first strand: chain 'Q' and resid 103 through 106 Processing sheet with id= AR, first strand: chain 'Q' and resid 297 through 300 removed outlier: 6.830A pdb=" N ILE Q 151 " --> pdb=" O VAL Q 298 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER Q 300 " --> pdb=" O ILE Q 151 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU Q 153 " --> pdb=" O SER Q 300 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL Q 152 " --> pdb=" O VAL Q 163 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id= AT, first strand: chain 'R' and resid 8 through 10 removed outlier: 4.140A pdb=" N THR R 106 " --> pdb=" O CYS R 10 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'R' and resid 16 through 19 removed outlier: 3.527A pdb=" N ALA R 29 " --> pdb=" O ALA R 19 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'R' and resid 35 through 38 removed outlier: 3.537A pdb=" N VAL R 35 " --> pdb=" O LYS R 68 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG R 37 " --> pdb=" O THR R 66 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'R' and resid 298 through 300 removed outlier: 3.684A pdb=" N VAL R 152 " --> pdb=" O VAL R 163 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL R 163 " --> pdb=" O VAL R 152 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP R 154 " --> pdb=" O HIS R 161 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS R 161 " --> pdb=" O ASP R 154 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'R' and resid 238 through 241 removed outlier: 3.523A pdb=" N LYS R 238 " --> pdb=" O ILE R 250 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'H' and resid 8 through 12 removed outlier: 3.594A pdb=" N LYS H 18 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 65 through 69 removed outlier: 4.102A pdb=" N ARG H 37 " --> pdb=" O THR H 66 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS H 68 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL H 35 " --> pdb=" O LYS H 68 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'H' and resid 103 through 107 removed outlier: 3.714A pdb=" N TYR H 133 " --> pdb=" O THR H 103 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'H' and resid 297 through 300 removed outlier: 6.080A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'H' and resid 238 through 241 Processing sheet with id= BD, first strand: chain 'I' and resid 29 through 32 removed outlier: 3.551A pdb=" N PHE I 31 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N CYS I 10 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU I 104 " --> pdb=" O CYS I 10 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN I 12 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR I 106 " --> pdb=" O ASN I 12 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'I' and resid 35 through 37 Processing sheet with id= BF, first strand: chain 'I' and resid 298 through 300 removed outlier: 3.566A pdb=" N SER I 300 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER I 155 " --> pdb=" O SER I 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET I 176 " --> pdb=" O ASN I 162 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'I' and resid 238 through 241 1398 hydrogen bonds defined for protein. 3642 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: 14.34 Time building geometry restraints manager: 18.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 12245 1.33 - 1.45: 5879 1.45 - 1.57: 21477 1.57 - 1.69: 32 1.69 - 1.81: 395 Bond restraints: 40028 Sorted by residual: bond pdb=" C4 ATP B 902 " pdb=" C5 ATP B 902 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.33e+01 bond pdb=" C5 ATP B 902 " pdb=" C6 ATP B 902 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 bond pdb=" C4 ADP A 902 " pdb=" C5 ADP A 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C8 ATP B 902 " pdb=" N7 ATP B 902 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" C4 ATP B 902 " pdb=" N9 ATP B 902 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.90e+01 ... (remaining 40023 not shown) Histogram of bond angle deviations from ideal: 98.72 - 106.18: 1264 106.18 - 113.65: 21885 113.65 - 121.11: 20246 121.11 - 128.58: 10669 128.58 - 136.04: 262 Bond angle restraints: 54326 Sorted by residual: angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 120.73 19.14 1.00e+00 1.00e+00 3.66e+02 angle pdb=" PA ATP B 902 " pdb=" O3A ATP B 902 " pdb=" PB ATP B 902 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP B 902 " pdb=" C4 ATP B 902 " pdb=" N3 ATP B 902 " ideal model delta sigma weight residual 126.80 118.83 7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" N3 ATP B 902 " pdb=" C4 ATP B 902 " pdb=" N9 ATP B 902 " ideal model delta sigma weight residual 127.04 134.92 -7.88 1.15e+00 7.59e-01 4.72e+01 angle pdb=" N GLU N 253 " pdb=" CA GLU N 253 " pdb=" C GLU N 253 " ideal model delta sigma weight residual 112.38 119.99 -7.61 1.22e+00 6.72e-01 3.89e+01 ... (remaining 54321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 23443 33.36 - 66.73: 587 66.73 - 100.09: 57 100.09 - 133.45: 4 133.45 - 166.82: 8 Dihedral angle restraints: 24099 sinusoidal: 9778 harmonic: 14321 Sorted by residual: dihedral pdb=" CD ARG D 205 " pdb=" NE ARG D 205 " pdb=" CZ ARG D 205 " pdb=" NH1 ARG D 205 " ideal model delta sinusoidal sigma weight residual 0.00 -86.73 86.73 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CD ARG D 204 " pdb=" NE ARG D 204 " pdb=" CZ ARG D 204 " pdb=" NH1 ARG D 204 " ideal model delta sinusoidal sigma weight residual 0.00 67.42 -67.42 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CD ARG N 256 " pdb=" NE ARG N 256 " pdb=" CZ ARG N 256 " pdb=" NH1 ARG N 256 " ideal model delta sinusoidal sigma weight residual 0.00 -63.68 63.68 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 24096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 5111 0.065 - 0.130: 870 0.130 - 0.195: 31 0.195 - 0.260: 3 0.260 - 0.325: 1 Chirality restraints: 6016 Sorted by residual: chirality pdb=" CA PHE N 255 " pdb=" N PHE N 255 " pdb=" C PHE N 255 " pdb=" CB PHE N 255 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA GLU N 253 " pdb=" N GLU N 253 " pdb=" C GLU N 253 " pdb=" CB GLU N 253 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ARG D 162 " pdb=" N ARG D 162 " pdb=" C ARG D 162 " pdb=" CB ARG D 162 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 6013 not shown) Planarity restraints: 6988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 205 " 1.097 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG D 205 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 205 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 205 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 205 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 204 " 1.017 9.50e-02 1.11e+02 4.56e-01 1.25e+02 pdb=" NE ARG D 204 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG D 204 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 204 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 204 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 256 " 0.987 9.50e-02 1.11e+02 4.42e-01 1.18e+02 pdb=" NE ARG N 256 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG N 256 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG N 256 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG N 256 " 0.024 2.00e-02 2.50e+03 ... (remaining 6985 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 399 2.60 - 3.17: 34672 3.17 - 3.75: 61238 3.75 - 4.32: 83737 4.32 - 4.90: 139388 Nonbonded interactions: 319434 Sorted by model distance: nonbonded pdb="MG MG R 801 " pdb=" O3B ADP R 802 " model vdw 2.023 2.170 nonbonded pdb="MG MG M 801 " pdb=" O3B ADP M 802 " model vdw 2.025 2.170 nonbonded pdb="MG MG Q 801 " pdb=" O3B ADP Q 802 " model vdw 2.048 2.170 nonbonded pdb="MG MG P 801 " pdb=" O3B ADP P 802 " model vdw 2.070 2.170 nonbonded pdb="MG MG N 801 " pdb=" O3B ADP N 802 " model vdw 2.086 2.170 ... (remaining 319429 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 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 7.900 Check model and map are aligned: 0.520 Set scattering table: 0.350 Process input model: 102.180 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.004 0.110 40028 Z= 0.242 Angle : 0.707 19.141 54326 Z= 0.393 Chirality : 0.046 0.325 6016 Planarity : 0.011 0.492 6988 Dihedral : 15.386 166.817 14894 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 0.24 % Allowed : 0.43 % Favored : 99.34 % Cbeta Deviations : 0.02 % 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: 0.07 (0.13), residues: 4875 helix: 0.98 (0.12), residues: 1833 sheet: -0.62 (0.17), residues: 960 loop : -0.34 (0.15), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.003 TRP Q 340 HIS 0.010 0.001 HIS H 87 PHE 0.030 0.001 PHE M 352 TYR 0.034 0.001 TYR H 166 ARG 0.013 0.001 ARG I 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1266 time to evaluate : 4.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5108 (m-80) cc_final: 0.4436 (m-80) REVERT: A 18 LYS cc_start: 0.7589 (mtmt) cc_final: 0.7330 (mptt) REVERT: A 140 GLU cc_start: 0.8335 (tt0) cc_final: 0.7880 (pt0) REVERT: A 151 ASN cc_start: 0.6197 (t0) cc_final: 0.5756 (t0) REVERT: A 214 ARG cc_start: 0.6847 (ttt90) cc_final: 0.6583 (ttm170) REVERT: A 267 LYS cc_start: 0.7259 (mtpp) cc_final: 0.6825 (mtpp) REVERT: A 284 PHE cc_start: 0.6987 (p90) cc_final: 0.6475 (p90) REVERT: A 295 ASN cc_start: 0.8120 (t0) cc_final: 0.7310 (t0) REVERT: A 368 LYS cc_start: 0.8067 (pptt) cc_final: 0.7085 (mmtm) REVERT: A 382 GLN cc_start: 0.8346 (mm110) cc_final: 0.7905 (mm-40) REVERT: B 19 TYR cc_start: 0.7808 (m-80) cc_final: 0.7232 (m-10) REVERT: B 23 ASN cc_start: 0.7370 (m-40) cc_final: 0.7027 (m-40) REVERT: B 59 GLU cc_start: 0.6978 (pp20) cc_final: 0.6331 (pt0) REVERT: B 64 LEU cc_start: 0.8076 (mp) cc_final: 0.7861 (mt) REVERT: B 81 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7675 (mt-10) REVERT: B 83 ASN cc_start: 0.8136 (m110) cc_final: 0.6977 (m-40) REVERT: B 111 ASN cc_start: 0.7788 (m-40) cc_final: 0.7571 (m-40) REVERT: B 133 TYR cc_start: 0.8061 (t80) cc_final: 0.7226 (t80) REVERT: B 183 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.7182 (ttp80) REVERT: B 211 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 271 GLN cc_start: 0.8781 (mt0) cc_final: 0.8404 (mt0) REVERT: B 283 GLN cc_start: 0.7705 (tp40) cc_final: 0.7417 (mm110) REVERT: B 320 LEU cc_start: 0.8164 (tp) cc_final: 0.7775 (tp) REVERT: B 329 ASP cc_start: 0.7855 (t0) cc_final: 0.7324 (m-30) REVERT: B 345 ARG cc_start: 0.7886 (mtt90) cc_final: 0.7671 (ptp-110) REVERT: C 46 LYS cc_start: 0.7722 (pttp) cc_final: 0.7084 (ttpp) REVERT: C 69 ARG cc_start: 0.6779 (mtm180) cc_final: 0.6423 (mtm-85) REVERT: C 75 GLN cc_start: 0.7527 (tt0) cc_final: 0.7194 (tt0) REVERT: C 91 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7813 (ttpt) REVERT: C 130 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7064 (mp0) REVERT: C 135 TRP cc_start: 0.7748 (m-10) cc_final: 0.7196 (m100) REVERT: C 155 HIS cc_start: 0.7830 (t-90) cc_final: 0.7204 (t-90) REVERT: C 160 LEU cc_start: 0.8497 (mt) cc_final: 0.8263 (mp) REVERT: C 165 CYS cc_start: 0.8072 (t) cc_final: 0.7800 (t) REVERT: C 248 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8496 (mttp) REVERT: C 282 SER cc_start: 0.8651 (t) cc_final: 0.8302 (m) REVERT: C 366 SER cc_start: 0.7729 (p) cc_final: 0.7421 (m) REVERT: D 8 ASN cc_start: 0.7897 (t0) cc_final: 0.7601 (t0) REVERT: D 86 TYR cc_start: 0.7952 (m-80) cc_final: 0.7365 (m-80) REVERT: D 109 MET cc_start: 0.8267 (tpp) cc_final: 0.7993 (tpp) REVERT: D 119 LEU cc_start: 0.7953 (tp) cc_final: 0.7691 (tp) REVERT: D 125 ARG cc_start: 0.7223 (ttt180) cc_final: 0.6864 (tmm-80) REVERT: D 186 GLU cc_start: 0.6357 (tm-30) cc_final: 0.6058 (tm-30) REVERT: D 254 ASN cc_start: 0.7393 (t0) cc_final: 0.7039 (t0) REVERT: E 93 GLU cc_start: 0.7587 (mp0) cc_final: 0.7136 (mp0) REVERT: E 97 ASN cc_start: 0.7704 (m-40) cc_final: 0.7197 (m-40) REVERT: E 98 SER cc_start: 0.8163 (t) cc_final: 0.7717 (p) REVERT: F 3 ASN cc_start: 0.7785 (t0) cc_final: 0.7561 (m-40) REVERT: F 79 VAL cc_start: 0.9039 (t) cc_final: 0.8548 (m) REVERT: F 107 LYS cc_start: 0.8269 (mmmm) cc_final: 0.8019 (mtmt) REVERT: F 137 GLU cc_start: 0.7517 (tp30) cc_final: 0.7070 (tp30) REVERT: F 149 MET cc_start: 0.7620 (mtm) cc_final: 0.7260 (mtm) REVERT: G 100 SER cc_start: 0.7374 (p) cc_final: 0.6686 (t) REVERT: G 119 GLN cc_start: 0.8677 (pp30) cc_final: 0.8006 (pp30) REVERT: G 135 GLU cc_start: 0.8437 (tt0) cc_final: 0.8054 (pt0) REVERT: G 151 ASP cc_start: 0.6446 (p0) cc_final: 0.5778 (p0) REVERT: M 122 ILE cc_start: 0.7950 (mt) cc_final: 0.7623 (mm) REVERT: M 123 MET cc_start: 0.8213 (tpt) cc_final: 0.7433 (ttm) REVERT: M 128 ASN cc_start: 0.8368 (t0) cc_final: 0.8005 (m-40) REVERT: M 263 GLN cc_start: 0.8285 (mt0) cc_final: 0.7884 (mt0) REVERT: N 44 MET cc_start: 0.5012 (tpt) cc_final: 0.4795 (mtp) REVERT: N 82 MET cc_start: 0.8497 (tpp) cc_final: 0.8283 (tpt) REVERT: N 113 LYS cc_start: 0.8419 (ptpt) cc_final: 0.8197 (ptmt) REVERT: N 257 CYS cc_start: 0.7165 (t) cc_final: 0.6810 (t) REVERT: N 296 ASN cc_start: 0.7225 (m110) cc_final: 0.6936 (m-40) REVERT: N 316 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7901 (mm-30) REVERT: O 59 GLN cc_start: 0.8649 (tp40) cc_final: 0.8318 (mm-40) REVERT: O 149 THR cc_start: 0.7997 (p) cc_final: 0.7565 (t) REVERT: O 154 ASP cc_start: 0.7754 (t0) cc_final: 0.7424 (t0) REVERT: O 157 ASP cc_start: 0.8458 (t70) cc_final: 0.8031 (t0) REVERT: O 176 MET cc_start: 0.8179 (mmm) cc_final: 0.7654 (mmm) REVERT: O 242 LEU cc_start: 0.8825 (tp) cc_final: 0.8399 (mt) REVERT: O 253 GLU cc_start: 0.8147 (mp0) cc_final: 0.7896 (mp0) REVERT: O 263 GLN cc_start: 0.8616 (mt0) cc_final: 0.8357 (mt0) REVERT: O 299 MET cc_start: 0.8125 (mmm) cc_final: 0.7916 (mmm) REVERT: P 47 MET cc_start: 0.7010 (pmm) cc_final: 0.6382 (pmm) REVERT: P 69 TYR cc_start: 0.8388 (m-80) cc_final: 0.8118 (m-80) REVERT: P 89 THR cc_start: 0.8640 (m) cc_final: 0.8316 (p) REVERT: P 117 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7732 (mt-10) REVERT: P 121 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8217 (tm-30) REVERT: P 180 LEU cc_start: 0.9078 (tp) cc_final: 0.8863 (tp) REVERT: P 227 MET cc_start: 0.8794 (mmm) cc_final: 0.8355 (mmt) REVERT: P 299 MET cc_start: 0.8295 (mmm) cc_final: 0.8030 (tpt) REVERT: Q 47 MET cc_start: 0.7061 (mmm) cc_final: 0.5818 (ptt) REVERT: Q 59 GLN cc_start: 0.8659 (tp40) cc_final: 0.8167 (tm-30) REVERT: Q 106 THR cc_start: 0.8944 (m) cc_final: 0.8697 (p) REVERT: Q 132 MET cc_start: 0.7748 (ppp) cc_final: 0.7502 (ppp) REVERT: Q 227 MET cc_start: 0.8529 (mmm) cc_final: 0.8279 (mmm) REVERT: Q 283 MET cc_start: 0.8298 (mmm) cc_final: 0.7987 (mmp) REVERT: R 113 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7420 (mttp) REVERT: R 132 MET cc_start: 0.7831 (ppp) cc_final: 0.7380 (ppp) REVERT: R 208 ILE cc_start: 0.8638 (mt) cc_final: 0.8393 (mm) REVERT: R 229 THR cc_start: 0.7518 (m) cc_final: 0.7316 (m) REVERT: R 288 ASP cc_start: 0.5927 (p0) cc_final: 0.5617 (t0) REVERT: R 337 TYR cc_start: 0.8811 (m-80) cc_final: 0.8531 (m-80) REVERT: H 92 ASN cc_start: 0.7450 (m110) cc_final: 0.7101 (m110) REVERT: H 121 GLN cc_start: 0.8348 (tm130) cc_final: 0.8102 (tm-30) REVERT: H 180 LEU cc_start: 0.8302 (mt) cc_final: 0.7895 (mt) REVERT: H 236 LEU cc_start: 0.7856 (pt) cc_final: 0.7555 (mt) REVERT: H 237 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6134 (tp30) REVERT: H 238 LYS cc_start: 0.7152 (mmmm) cc_final: 0.6893 (mptt) REVERT: H 249 THR cc_start: 0.7696 (m) cc_final: 0.7178 (p) REVERT: H 286 ASP cc_start: 0.6854 (p0) cc_final: 0.6632 (p0) REVERT: H 294 TYR cc_start: 0.6952 (m-80) cc_final: 0.6566 (m-10) REVERT: H 313 MET cc_start: 0.8454 (tpt) cc_final: 0.8003 (tpp) REVERT: H 329 ILE cc_start: 0.8294 (mm) cc_final: 0.7755 (mt) REVERT: H 352 PHE cc_start: 0.7790 (t80) cc_final: 0.7479 (t80) REVERT: H 355 MET cc_start: 0.7142 (pmm) cc_final: 0.6899 (pmm) REVERT: H 367 PRO cc_start: 0.8009 (Cg_endo) cc_final: 0.7201 (Cg_exo) REVERT: I 12 ASN cc_start: 0.7546 (p0) cc_final: 0.7284 (p0) REVERT: I 62 ARG cc_start: 0.8235 (ptt180) cc_final: 0.7989 (ptp90) REVERT: I 107 GLU cc_start: 0.7472 (pm20) cc_final: 0.7054 (pm20) REVERT: I 153 LEU cc_start: 0.7638 (tp) cc_final: 0.7212 (tt) REVERT: I 173 HIS cc_start: 0.6260 (m170) cc_final: 0.5869 (m170) REVERT: I 222 ASP cc_start: 0.6548 (p0) cc_final: 0.6169 (p0) REVERT: I 227 MET cc_start: 0.7810 (ttt) cc_final: 0.7111 (mtp) REVERT: I 236 LEU cc_start: 0.7323 (pp) cc_final: 0.7033 (mt) REVERT: I 237 GLU cc_start: 0.6244 (mt-10) cc_final: 0.5917 (mt-10) REVERT: I 241 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7135 (tm-30) REVERT: I 263 GLN cc_start: 0.8593 (mt0) cc_final: 0.8094 (mt0) REVERT: I 280 ASN cc_start: 0.7437 (m-40) cc_final: 0.7106 (m-40) REVERT: I 296 ASN cc_start: 0.5598 (t0) cc_final: 0.5341 (t0) REVERT: I 325 MET cc_start: 0.6316 (ppp) cc_final: 0.5985 (ppp) REVERT: I 352 PHE cc_start: 0.6539 (t80) cc_final: 0.6294 (t80) outliers start: 10 outliers final: 2 residues processed: 1270 average time/residue: 0.5707 time to fit residues: 1145.2186 Evaluate side-chains 724 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 722 time to evaluate : 4.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain R residue 136 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 0.4980 chunk 369 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 249 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 382 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 443 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 221 GLN A 316 GLN B 319 GLN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN D 296 ASN F 58 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN M 296 ASN N 92 ASN N 162 ASN O 49 GLN O 88 HIS O 161 HIS Q 40 HIS Q 111 ASN R 12 ASN R 92 ASN R 111 ASN R 161 HIS ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 173 HIS H 246 GLN ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN I 162 ASN I 354 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 40028 Z= 0.387 Angle : 0.738 15.125 54326 Z= 0.370 Chirality : 0.049 0.181 6016 Planarity : 0.006 0.163 6988 Dihedral : 9.079 178.085 5548 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.70 % Favored : 94.28 % Rotamer: Outliers : 2.40 % Allowed : 13.93 % Favored : 83.68 % 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: -0.30 (0.12), residues: 4875 helix: 0.60 (0.12), residues: 1792 sheet: -0.73 (0.17), residues: 974 loop : -0.49 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP Q 340 HIS 0.008 0.002 HIS A 404 PHE 0.022 0.002 PHE A 150 TYR 0.026 0.002 TYR R 166 ARG 0.019 0.001 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 704 time to evaluate : 4.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5211 (m-80) cc_final: 0.4552 (m-80) REVERT: A 133 LEU cc_start: 0.7876 (mp) cc_final: 0.7245 (tp) REVERT: A 140 GLU cc_start: 0.8469 (tt0) cc_final: 0.7991 (pt0) REVERT: A 214 ARG cc_start: 0.7084 (ttt90) cc_final: 0.6710 (ttm170) REVERT: A 243 GLU cc_start: 0.7228 (pm20) cc_final: 0.6777 (pm20) REVERT: A 281 ASP cc_start: 0.8153 (t0) cc_final: 0.7750 (t0) REVERT: A 284 PHE cc_start: 0.7399 (p90) cc_final: 0.6837 (p90) REVERT: A 295 ASN cc_start: 0.8141 (t0) cc_final: 0.7515 (t0) REVERT: A 368 LYS cc_start: 0.7951 (pptt) cc_final: 0.6851 (mmtm) REVERT: A 382 GLN cc_start: 0.8392 (mm110) cc_final: 0.8143 (tp-100) REVERT: A 420 TYR cc_start: 0.5049 (t80) cc_final: 0.4556 (t80) REVERT: B 19 TYR cc_start: 0.7809 (m-80) cc_final: 0.7374 (m-10) REVERT: B 51 ASP cc_start: 0.6745 (t0) cc_final: 0.6543 (t0) REVERT: B 64 LEU cc_start: 0.8124 (mp) cc_final: 0.7920 (mt) REVERT: B 72 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6284 (pm20) REVERT: B 81 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 86 TRP cc_start: 0.8766 (m-90) cc_final: 0.7889 (m-90) REVERT: B 183 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7183 (ttp80) REVERT: B 227 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7219 (t-90) REVERT: B 283 GLN cc_start: 0.7945 (tp40) cc_final: 0.7407 (mm110) REVERT: B 324 ARG cc_start: 0.7200 (tpp80) cc_final: 0.6966 (tpp80) REVERT: B 329 ASP cc_start: 0.7979 (t0) cc_final: 0.7454 (m-30) REVERT: C 69 ARG cc_start: 0.6614 (mtm180) cc_final: 0.5749 (mtm-85) REVERT: C 75 GLN cc_start: 0.7507 (tt0) cc_final: 0.7285 (tt0) REVERT: C 155 HIS cc_start: 0.8155 (t-90) cc_final: 0.7488 (t-90) REVERT: C 165 CYS cc_start: 0.8189 (t) cc_final: 0.7646 (t) REVERT: D 8 ASN cc_start: 0.8273 (t0) cc_final: 0.7815 (t0) REVERT: D 57 LYS cc_start: 0.7555 (ptmt) cc_final: 0.7122 (ptpp) REVERT: D 119 LEU cc_start: 0.8308 (tp) cc_final: 0.8100 (tp) REVERT: D 125 ARG cc_start: 0.7091 (ttt180) cc_final: 0.6835 (tmm-80) REVERT: D 129 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7552 (mmtp) REVERT: D 148 ASP cc_start: 0.6141 (m-30) cc_final: 0.5921 (m-30) REVERT: D 161 TYR cc_start: 0.7267 (p90) cc_final: 0.6983 (p90) REVERT: D 254 ASN cc_start: 0.7661 (t0) cc_final: 0.6651 (t0) REVERT: D 280 MET cc_start: 0.8555 (mmt) cc_final: 0.8285 (mmt) REVERT: E 22 MET cc_start: 0.5149 (OUTLIER) cc_final: 0.4545 (tmm) REVERT: E 79 GLU cc_start: 0.6032 (tp30) cc_final: 0.5455 (tp30) REVERT: E 83 ARG cc_start: 0.5098 (tpp80) cc_final: 0.4795 (tpp80) REVERT: E 93 GLU cc_start: 0.7913 (mp0) cc_final: 0.7664 (mp0) REVERT: E 97 ASN cc_start: 0.7958 (m-40) cc_final: 0.7506 (m-40) REVERT: E 98 SER cc_start: 0.7957 (t) cc_final: 0.7490 (p) REVERT: F 3 ASN cc_start: 0.7864 (t0) cc_final: 0.7643 (t0) REVERT: F 58 GLN cc_start: 0.8042 (mp-120) cc_final: 0.7814 (mp10) REVERT: F 77 LYS cc_start: 0.7819 (tppt) cc_final: 0.7608 (tppt) REVERT: F 79 VAL cc_start: 0.8982 (t) cc_final: 0.8700 (m) REVERT: F 89 LYS cc_start: 0.7863 (tppp) cc_final: 0.7357 (ttpt) REVERT: F 119 THR cc_start: 0.8764 (m) cc_final: 0.8245 (p) REVERT: F 137 GLU cc_start: 0.7625 (tp30) cc_final: 0.6873 (tp30) REVERT: G 30 GLU cc_start: 0.7764 (mp0) cc_final: 0.7555 (mm-30) REVERT: G 82 ASP cc_start: 0.8205 (m-30) cc_final: 0.7916 (m-30) REVERT: G 117 ASN cc_start: 0.7102 (t0) cc_final: 0.6698 (p0) REVERT: G 119 GLN cc_start: 0.8401 (pp30) cc_final: 0.8146 (pm20) REVERT: G 151 ASP cc_start: 0.6337 (p0) cc_final: 0.5777 (p0) REVERT: M 122 ILE cc_start: 0.8094 (mt) cc_final: 0.7800 (mm) REVERT: M 128 ASN cc_start: 0.8493 (t0) cc_final: 0.8054 (m-40) REVERT: M 283 MET cc_start: 0.8145 (mmm) cc_final: 0.7906 (mmm) REVERT: N 44 MET cc_start: 0.5021 (tpt) cc_final: 0.4418 (mtm) REVERT: N 113 LYS cc_start: 0.8343 (ptpt) cc_final: 0.8078 (mmmt) REVERT: N 316 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7972 (mm-30) REVERT: O 154 ASP cc_start: 0.7754 (t0) cc_final: 0.7551 (t0) REVERT: O 157 ASP cc_start: 0.8608 (t70) cc_final: 0.8218 (t0) REVERT: O 242 LEU cc_start: 0.8815 (tp) cc_final: 0.8586 (mt) REVERT: O 253 GLU cc_start: 0.8371 (mp0) cc_final: 0.7957 (mp0) REVERT: O 337 TYR cc_start: 0.8410 (m-80) cc_final: 0.8039 (m-80) REVERT: P 69 TYR cc_start: 0.8373 (m-80) cc_final: 0.8009 (m-80) REVERT: P 89 THR cc_start: 0.8766 (m) cc_final: 0.8289 (p) REVERT: P 121 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8160 (tm-30) REVERT: P 227 MET cc_start: 0.8911 (mmm) cc_final: 0.8530 (mmt) REVERT: Q 44 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8482 (mmt) REVERT: Q 47 MET cc_start: 0.7229 (mmm) cc_final: 0.5876 (ptp) REVERT: Q 59 GLN cc_start: 0.8716 (tp40) cc_final: 0.8115 (tm-30) REVERT: Q 103 THR cc_start: 0.9270 (t) cc_final: 0.9032 (p) REVERT: Q 227 MET cc_start: 0.8622 (mmm) cc_final: 0.8311 (mmm) REVERT: Q 283 MET cc_start: 0.8541 (mmm) cc_final: 0.7971 (mmt) REVERT: R 137 GLN cc_start: 0.8099 (mt0) cc_final: 0.7588 (mp10) REVERT: H 123 MET cc_start: 0.8005 (ttm) cc_final: 0.7671 (ttm) REVERT: H 140 LEU cc_start: 0.8728 (mt) cc_final: 0.8435 (mp) REVERT: H 236 LEU cc_start: 0.7881 (pt) cc_final: 0.7348 (mt) REVERT: H 237 GLU cc_start: 0.7607 (mm-30) cc_final: 0.6609 (tm-30) REVERT: H 238 LYS cc_start: 0.7113 (mmmm) cc_final: 0.6377 (mptt) REVERT: H 249 THR cc_start: 0.8132 (m) cc_final: 0.7744 (p) REVERT: H 288 ASP cc_start: 0.3863 (t0) cc_final: 0.3598 (t0) REVERT: H 294 TYR cc_start: 0.6970 (m-80) cc_final: 0.6769 (m-10) REVERT: H 299 MET cc_start: 0.6817 (mtp) cc_final: 0.6397 (mtp) REVERT: H 311 ASP cc_start: 0.7637 (m-30) cc_final: 0.7292 (m-30) REVERT: H 313 MET cc_start: 0.8417 (tpt) cc_final: 0.7990 (tpp) REVERT: H 329 ILE cc_start: 0.8162 (mm) cc_final: 0.7707 (mt) REVERT: H 352 PHE cc_start: 0.7913 (t80) cc_final: 0.7013 (t80) REVERT: H 356 TRP cc_start: 0.7565 (m100) cc_final: 0.6450 (m100) REVERT: I 82 MET cc_start: 0.8208 (mmt) cc_final: 0.7871 (mmm) REVERT: I 222 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6037 (p0) REVERT: I 241 GLU cc_start: 0.7852 (tm-30) cc_final: 0.6978 (tm-30) REVERT: I 244 ASP cc_start: 0.7093 (p0) cc_final: 0.6844 (p0) REVERT: I 280 ASN cc_start: 0.7598 (m-40) cc_final: 0.7037 (m-40) REVERT: I 296 ASN cc_start: 0.5634 (t0) cc_final: 0.5281 (t0) REVERT: I 325 MET cc_start: 0.6748 (ppp) cc_final: 0.6003 (ppp) outliers start: 101 outliers final: 69 residues processed: 765 average time/residue: 0.5343 time to fit residues: 652.1332 Evaluate side-chains 678 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 604 time to evaluate : 4.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain N residue 92 ASN Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 238 LYS Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 GLN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 354 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 368 optimal weight: 0.0770 chunk 301 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 443 optimal weight: 0.1980 chunk 479 optimal weight: 9.9990 chunk 395 optimal weight: 1.9990 chunk 440 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 356 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN N 92 ASN N 161 HIS ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 GLN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS H 246 GLN ** H 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40028 Z= 0.164 Angle : 0.599 14.010 54326 Z= 0.295 Chirality : 0.044 0.172 6016 Planarity : 0.004 0.049 6988 Dihedral : 8.614 174.501 5545 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 2.09 % Allowed : 16.04 % Favored : 81.87 % 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: -0.07 (0.12), residues: 4875 helix: 0.79 (0.12), residues: 1793 sheet: -0.54 (0.17), residues: 949 loop : -0.40 (0.14), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 340 HIS 0.005 0.001 HIS A 192 PHE 0.018 0.001 PHE F 25 TYR 0.020 0.001 TYR R 166 ARG 0.007 0.001 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 673 time to evaluate : 4.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7372 (ttmm) REVERT: A 101 ASN cc_start: 0.6690 (t0) cc_final: 0.6448 (t0) REVERT: A 133 LEU cc_start: 0.7590 (mp) cc_final: 0.6969 (tp) REVERT: A 140 GLU cc_start: 0.8413 (tt0) cc_final: 0.8072 (pt0) REVERT: A 214 ARG cc_start: 0.7023 (ttt90) cc_final: 0.6654 (ttm170) REVERT: A 243 GLU cc_start: 0.6818 (pm20) cc_final: 0.6582 (pm20) REVERT: A 281 ASP cc_start: 0.8256 (t0) cc_final: 0.7827 (t0) REVERT: A 284 PHE cc_start: 0.7153 (p90) cc_final: 0.6685 (p90) REVERT: A 295 ASN cc_start: 0.8114 (t0) cc_final: 0.7524 (t0) REVERT: A 368 LYS cc_start: 0.7943 (pptt) cc_final: 0.6941 (mmtm) REVERT: A 382 GLN cc_start: 0.8378 (mm110) cc_final: 0.7777 (tp-100) REVERT: A 420 TYR cc_start: 0.4797 (t80) cc_final: 0.4425 (t80) REVERT: B 19 TYR cc_start: 0.7833 (m-80) cc_final: 0.7409 (m-10) REVERT: B 51 ASP cc_start: 0.6427 (t0) cc_final: 0.6121 (t0) REVERT: B 64 LEU cc_start: 0.8042 (mp) cc_final: 0.7827 (mt) REVERT: B 81 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 119 MET cc_start: 0.7633 (ttt) cc_final: 0.7259 (ttp) REVERT: B 133 TYR cc_start: 0.8078 (t80) cc_final: 0.7005 (t80) REVERT: B 162 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8597 (pp) REVERT: B 227 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7146 (t-90) REVERT: B 283 GLN cc_start: 0.7788 (tp40) cc_final: 0.7277 (mm110) REVERT: B 324 ARG cc_start: 0.7156 (tpp80) cc_final: 0.6798 (tpp80) REVERT: B 329 ASP cc_start: 0.7989 (t0) cc_final: 0.7484 (m-30) REVERT: C 75 GLN cc_start: 0.7383 (tt0) cc_final: 0.7090 (tt0) REVERT: C 155 HIS cc_start: 0.7958 (t-90) cc_final: 0.7235 (t-90) REVERT: C 165 CYS cc_start: 0.8112 (t) cc_final: 0.7588 (t) REVERT: D 8 ASN cc_start: 0.8165 (t0) cc_final: 0.7942 (t0) REVERT: D 57 LYS cc_start: 0.7468 (ptmt) cc_final: 0.7065 (ptpp) REVERT: D 64 ASN cc_start: 0.8091 (t0) cc_final: 0.7430 (m-40) REVERT: D 113 MET cc_start: 0.7481 (tpp) cc_final: 0.7272 (tpp) REVERT: D 118 VAL cc_start: 0.8109 (p) cc_final: 0.7900 (p) REVERT: D 119 LEU cc_start: 0.8316 (tp) cc_final: 0.8029 (tp) REVERT: D 125 ARG cc_start: 0.7142 (ttt180) cc_final: 0.6791 (tmm-80) REVERT: D 129 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7575 (mmtp) REVERT: D 254 ASN cc_start: 0.7640 (t0) cc_final: 0.6633 (t0) REVERT: D 280 MET cc_start: 0.8386 (mmt) cc_final: 0.7987 (mmt) REVERT: E 79 GLU cc_start: 0.6060 (tp30) cc_final: 0.5388 (tp30) REVERT: E 83 ARG cc_start: 0.5070 (tpp80) cc_final: 0.4777 (tpp80) REVERT: E 93 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: E 97 ASN cc_start: 0.8041 (m-40) cc_final: 0.7718 (m-40) REVERT: E 98 SER cc_start: 0.8045 (t) cc_final: 0.7494 (p) REVERT: F 58 GLN cc_start: 0.7944 (mp-120) cc_final: 0.7702 (mp10) REVERT: F 77 LYS cc_start: 0.7738 (tppt) cc_final: 0.7255 (tppt) REVERT: F 89 LYS cc_start: 0.7854 (tppp) cc_final: 0.7264 (ttpt) REVERT: F 137 GLU cc_start: 0.7562 (tp30) cc_final: 0.7318 (mt-10) REVERT: G 75 GLN cc_start: 0.8297 (mm-40) cc_final: 0.8093 (mm-40) REVERT: G 82 ASP cc_start: 0.8284 (m-30) cc_final: 0.8017 (m-30) REVERT: G 117 ASN cc_start: 0.7101 (t0) cc_final: 0.6715 (p0) REVERT: G 119 GLN cc_start: 0.8485 (pp30) cc_final: 0.8104 (pm20) REVERT: G 129 TRP cc_start: 0.7891 (m100) cc_final: 0.7676 (m100) REVERT: G 151 ASP cc_start: 0.6509 (p0) cc_final: 0.5990 (p0) REVERT: M 122 ILE cc_start: 0.8006 (mt) cc_final: 0.7700 (mm) REVERT: M 128 ASN cc_start: 0.8487 (t0) cc_final: 0.7966 (m-40) REVERT: M 283 MET cc_start: 0.8218 (mmm) cc_final: 0.8017 (mmm) REVERT: M 325 MET cc_start: 0.7542 (ptm) cc_final: 0.7313 (ptm) REVERT: N 44 MET cc_start: 0.4903 (tpt) cc_final: 0.4125 (mtm) REVERT: N 224 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7893 (mm-30) REVERT: O 84 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8540 (ttmt) REVERT: O 157 ASP cc_start: 0.8523 (t70) cc_final: 0.8062 (t0) REVERT: O 206 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7766 (ttp80) REVERT: O 242 LEU cc_start: 0.8783 (tp) cc_final: 0.8542 (mt) REVERT: O 253 GLU cc_start: 0.8262 (mp0) cc_final: 0.7740 (mp0) REVERT: O 330 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8108 (mt) REVERT: P 69 TYR cc_start: 0.8268 (m-80) cc_final: 0.7961 (m-80) REVERT: P 89 THR cc_start: 0.8683 (m) cc_final: 0.8322 (p) REVERT: P 121 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8102 (tm-30) REVERT: P 227 MET cc_start: 0.8930 (mmm) cc_final: 0.8289 (mmt) REVERT: P 286 ASP cc_start: 0.8088 (t70) cc_final: 0.7751 (t70) REVERT: Q 47 MET cc_start: 0.7043 (mmm) cc_final: 0.5892 (ptp) REVERT: Q 49 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6995 (tt0) REVERT: Q 59 GLN cc_start: 0.8667 (tp40) cc_final: 0.8101 (tm-30) REVERT: Q 227 MET cc_start: 0.8601 (mmm) cc_final: 0.8271 (mmm) REVERT: Q 283 MET cc_start: 0.8567 (mmm) cc_final: 0.8014 (mmt) REVERT: Q 346 LEU cc_start: 0.9170 (tp) cc_final: 0.8830 (tp) REVERT: R 113 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7270 (mptt) REVERT: R 137 GLN cc_start: 0.8083 (mt0) cc_final: 0.7600 (mp10) REVERT: H 121 GLN cc_start: 0.8090 (tm130) cc_final: 0.7823 (tm-30) REVERT: H 122 ILE cc_start: 0.8031 (tp) cc_final: 0.7768 (mm) REVERT: H 123 MET cc_start: 0.7980 (ttm) cc_final: 0.7356 (ttm) REVERT: H 140 LEU cc_start: 0.8717 (mt) cc_final: 0.8449 (mp) REVERT: H 236 LEU cc_start: 0.7732 (pt) cc_final: 0.7387 (mt) REVERT: H 237 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6892 (tm-30) REVERT: H 238 LYS cc_start: 0.7288 (mmmm) cc_final: 0.6505 (mptt) REVERT: H 249 THR cc_start: 0.8095 (m) cc_final: 0.7698 (p) REVERT: H 286 ASP cc_start: 0.7328 (p0) cc_final: 0.6362 (p0) REVERT: H 290 ARG cc_start: 0.7397 (mtm180) cc_final: 0.6703 (mtt90) REVERT: H 313 MET cc_start: 0.8252 (tpt) cc_final: 0.7933 (tpp) REVERT: H 352 PHE cc_start: 0.8167 (t80) cc_final: 0.7910 (t80) REVERT: H 353 GLN cc_start: 0.7172 (mp10) cc_final: 0.6893 (mp10) REVERT: H 355 MET cc_start: 0.7156 (pmm) cc_final: 0.6663 (pmm) REVERT: I 82 MET cc_start: 0.8234 (mmt) cc_final: 0.7897 (mmm) REVERT: I 116 ARG cc_start: 0.6799 (mmt180) cc_final: 0.6594 (mmt180) REVERT: I 222 ASP cc_start: 0.6436 (p0) cc_final: 0.5867 (p0) REVERT: I 241 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7084 (tm-30) REVERT: I 280 ASN cc_start: 0.7246 (m-40) cc_final: 0.6921 (m110) REVERT: I 296 ASN cc_start: 0.5633 (t0) cc_final: 0.5270 (t0) REVERT: I 325 MET cc_start: 0.6607 (ppp) cc_final: 0.5879 (ppp) outliers start: 88 outliers final: 52 residues processed: 730 average time/residue: 0.5405 time to fit residues: 639.2517 Evaluate side-chains 667 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 610 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 327 ILE Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 317 ILE Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 211 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 445 optimal weight: 2.9990 chunk 471 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 chunk 422 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS A 316 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 173 HIS H 297 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 40028 Z= 0.272 Angle : 0.620 13.132 54326 Z= 0.305 Chirality : 0.045 0.182 6016 Planarity : 0.004 0.047 6988 Dihedral : 8.482 170.845 5545 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.13 % Allowed : 17.15 % Favored : 79.72 % 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: -0.12 (0.12), residues: 4875 helix: 0.73 (0.12), residues: 1796 sheet: -0.59 (0.17), residues: 966 loop : -0.40 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 340 HIS 0.005 0.001 HIS C 286 PHE 0.019 0.001 PHE D 250 TYR 0.034 0.001 TYR G 112 ARG 0.014 0.001 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 615 time to evaluate : 4.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.4818 (OUTLIER) cc_final: 0.3484 (m-80) REVERT: A 83 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7638 (ttmm) REVERT: A 133 LEU cc_start: 0.7718 (mp) cc_final: 0.7141 (tp) REVERT: A 140 GLU cc_start: 0.8398 (tt0) cc_final: 0.8051 (pt0) REVERT: A 214 ARG cc_start: 0.7100 (ttt90) cc_final: 0.6747 (ttm170) REVERT: A 281 ASP cc_start: 0.8253 (t0) cc_final: 0.7811 (t0) REVERT: A 284 PHE cc_start: 0.7456 (p90) cc_final: 0.7019 (p90) REVERT: A 295 ASN cc_start: 0.8145 (t0) cc_final: 0.7534 (t0) REVERT: A 368 LYS cc_start: 0.7901 (pptt) cc_final: 0.6862 (mmtm) REVERT: A 382 GLN cc_start: 0.8443 (mm110) cc_final: 0.8185 (tp-100) REVERT: A 402 TYR cc_start: 0.7729 (m-10) cc_final: 0.7516 (m-10) REVERT: A 420 TYR cc_start: 0.4885 (t80) cc_final: 0.4646 (t80) REVERT: B 19 TYR cc_start: 0.7777 (m-80) cc_final: 0.7363 (m-10) REVERT: B 51 ASP cc_start: 0.6568 (t0) cc_final: 0.6182 (t0) REVERT: B 64 LEU cc_start: 0.8139 (mp) cc_final: 0.7907 (mt) REVERT: B 81 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7601 (mt-10) REVERT: B 82 MET cc_start: 0.8383 (tpt) cc_final: 0.7859 (tpt) REVERT: B 133 TYR cc_start: 0.8055 (t80) cc_final: 0.7021 (t80) REVERT: B 162 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8641 (pp) REVERT: B 227 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7211 (t-90) REVERT: B 324 ARG cc_start: 0.7122 (tpp80) cc_final: 0.6737 (tpp80) REVERT: B 329 ASP cc_start: 0.8025 (t0) cc_final: 0.7540 (m-30) REVERT: C 155 HIS cc_start: 0.7978 (t-90) cc_final: 0.7471 (t-90) REVERT: C 165 CYS cc_start: 0.8181 (t) cc_final: 0.7590 (t) REVERT: D 8 ASN cc_start: 0.8441 (t0) cc_final: 0.8193 (t0) REVERT: D 57 LYS cc_start: 0.7483 (ptmt) cc_final: 0.7052 (ptpp) REVERT: D 64 ASN cc_start: 0.8155 (t0) cc_final: 0.7507 (m-40) REVERT: D 119 LEU cc_start: 0.8290 (tp) cc_final: 0.8035 (tp) REVERT: D 129 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7671 (mmtp) REVERT: D 162 ARG cc_start: 0.7849 (tpp80) cc_final: 0.7375 (ttp-170) REVERT: E 61 GLU cc_start: 0.5887 (tp30) cc_final: 0.5395 (tp30) REVERT: E 93 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: E 97 ASN cc_start: 0.8072 (m-40) cc_final: 0.7748 (m-40) REVERT: E 98 SER cc_start: 0.8415 (t) cc_final: 0.7690 (p) REVERT: F 77 LYS cc_start: 0.7636 (tppt) cc_final: 0.7300 (tppt) REVERT: F 89 LYS cc_start: 0.7647 (tppp) cc_final: 0.7263 (ttpt) REVERT: F 137 GLU cc_start: 0.7564 (tp30) cc_final: 0.6928 (tp30) REVERT: G 27 GLU cc_start: 0.7530 (tt0) cc_final: 0.7066 (tt0) REVERT: G 75 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8138 (mm-40) REVERT: G 82 ASP cc_start: 0.8277 (m-30) cc_final: 0.8037 (m-30) REVERT: G 117 ASN cc_start: 0.7163 (t0) cc_final: 0.6696 (p0) REVERT: G 119 GLN cc_start: 0.8563 (pp30) cc_final: 0.8152 (pm20) REVERT: G 129 TRP cc_start: 0.7925 (m100) cc_final: 0.7692 (m100) REVERT: M 100 GLU cc_start: 0.7753 (pm20) cc_final: 0.7515 (pm20) REVERT: M 122 ILE cc_start: 0.8011 (mt) cc_final: 0.7723 (mm) REVERT: M 123 MET cc_start: 0.7761 (tpp) cc_final: 0.7494 (ttm) REVERT: M 128 ASN cc_start: 0.8474 (t0) cc_final: 0.7995 (m-40) REVERT: N 44 MET cc_start: 0.5081 (tpt) cc_final: 0.4154 (mtm) REVERT: N 224 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7965 (mm-30) REVERT: O 84 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8613 (ttmt) REVERT: O 157 ASP cc_start: 0.8519 (t70) cc_final: 0.8085 (t0) REVERT: O 206 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7686 (ttp80) REVERT: O 330 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8378 (mt) REVERT: P 69 TYR cc_start: 0.8292 (m-80) cc_final: 0.7973 (m-80) REVERT: P 89 THR cc_start: 0.8723 (m) cc_final: 0.8383 (p) REVERT: P 121 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8060 (tm-30) REVERT: P 227 MET cc_start: 0.8894 (mmm) cc_final: 0.8210 (mmt) REVERT: P 313 MET cc_start: 0.8212 (tpp) cc_final: 0.7899 (tpt) REVERT: P 316 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7842 (mm-30) REVERT: Q 47 MET cc_start: 0.7107 (mmm) cc_final: 0.5838 (ptp) REVERT: Q 59 GLN cc_start: 0.8640 (tp40) cc_final: 0.8238 (tm-30) REVERT: Q 227 MET cc_start: 0.8628 (mmm) cc_final: 0.8285 (mmm) REVERT: Q 283 MET cc_start: 0.8551 (mmm) cc_final: 0.7926 (mmp) REVERT: R 82 MET cc_start: 0.8853 (tpp) cc_final: 0.8359 (mmm) REVERT: R 137 GLN cc_start: 0.8157 (mt0) cc_final: 0.7602 (mp10) REVERT: R 269 MET cc_start: 0.8268 (ttm) cc_final: 0.7865 (ttm) REVERT: R 313 MET cc_start: 0.7746 (tpt) cc_final: 0.7525 (tpt) REVERT: H 44 MET cc_start: 0.4354 (tpt) cc_final: 0.3468 (tpt) REVERT: H 123 MET cc_start: 0.8083 (ttm) cc_final: 0.7611 (ttm) REVERT: H 140 LEU cc_start: 0.8745 (mt) cc_final: 0.8481 (mp) REVERT: H 236 LEU cc_start: 0.7902 (pt) cc_final: 0.7506 (mt) REVERT: H 238 LYS cc_start: 0.7098 (mmmm) cc_final: 0.6881 (mptt) REVERT: H 249 THR cc_start: 0.8200 (m) cc_final: 0.7716 (p) REVERT: H 355 MET cc_start: 0.6841 (pmm) cc_final: 0.6291 (pmm) REVERT: I 59 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7597 (tp40) REVERT: I 82 MET cc_start: 0.8286 (mmt) cc_final: 0.7916 (mmm) REVERT: I 178 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7363 (tt) REVERT: I 207 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7593 (mm-30) REVERT: I 222 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6022 (p0) REVERT: I 241 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7024 (tm-30) REVERT: I 280 ASN cc_start: 0.7293 (m-40) cc_final: 0.6990 (m110) REVERT: I 296 ASN cc_start: 0.5679 (t0) cc_final: 0.5346 (t0) REVERT: I 325 MET cc_start: 0.6548 (ppp) cc_final: 0.5845 (ppp) outliers start: 132 outliers final: 87 residues processed: 703 average time/residue: 0.5112 time to fit residues: 576.8683 Evaluate side-chains 683 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 589 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 20 ASP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 330 ILE Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 402 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 240 optimal weight: 0.7980 chunk 423 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 316 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN N 12 ASN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 297 ASN R 12 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS I 49 GLN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 40028 Z= 0.278 Angle : 0.621 12.736 54326 Z= 0.306 Chirality : 0.045 0.196 6016 Planarity : 0.004 0.048 6988 Dihedral : 8.321 163.826 5545 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.44 % Allowed : 18.13 % Favored : 78.43 % 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: -0.18 (0.12), residues: 4875 helix: 0.69 (0.12), residues: 1794 sheet: -0.64 (0.17), residues: 961 loop : -0.44 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 340 HIS 0.006 0.001 HIS R 275 PHE 0.024 0.002 PHE B 24 TYR 0.029 0.001 TYR G 112 ARG 0.007 0.001 ARG I 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 604 time to evaluate : 4.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.3686 (m-80) REVERT: A 83 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7754 (ttmm) REVERT: A 95 ARG cc_start: 0.7169 (ptp-170) cc_final: 0.6850 (ptp-170) REVERT: A 133 LEU cc_start: 0.7723 (mp) cc_final: 0.7096 (tp) REVERT: A 140 GLU cc_start: 0.8463 (tt0) cc_final: 0.8028 (pt0) REVERT: A 148 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7366 (mm-30) REVERT: A 194 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8655 (mm) REVERT: A 214 ARG cc_start: 0.7084 (ttt90) cc_final: 0.6704 (ttm170) REVERT: A 239 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.7535 (mpt-90) REVERT: A 281 ASP cc_start: 0.8273 (t0) cc_final: 0.7851 (t0) REVERT: A 284 PHE cc_start: 0.7460 (p90) cc_final: 0.6923 (p90) REVERT: A 295 ASN cc_start: 0.8178 (t0) cc_final: 0.7597 (t0) REVERT: A 368 LYS cc_start: 0.7876 (pptt) cc_final: 0.6825 (mmtm) REVERT: A 382 GLN cc_start: 0.8446 (mm110) cc_final: 0.8172 (tp-100) REVERT: A 402 TYR cc_start: 0.7848 (m-10) cc_final: 0.7607 (m-10) REVERT: A 420 TYR cc_start: 0.4767 (t80) cc_final: 0.4511 (t80) REVERT: B 19 TYR cc_start: 0.7736 (m-80) cc_final: 0.7297 (m-10) REVERT: B 51 ASP cc_start: 0.6392 (t0) cc_final: 0.6161 (t0) REVERT: B 64 LEU cc_start: 0.8136 (mp) cc_final: 0.7910 (mt) REVERT: B 85 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8470 (tt) REVERT: B 133 TYR cc_start: 0.8162 (t80) cc_final: 0.7219 (t80) REVERT: B 162 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8643 (pp) REVERT: B 227 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7260 (t-90) REVERT: B 283 GLN cc_start: 0.7880 (tp40) cc_final: 0.7345 (mm110) REVERT: B 320 LEU cc_start: 0.8083 (tp) cc_final: 0.7806 (tp) REVERT: B 324 ARG cc_start: 0.7212 (tpp80) cc_final: 0.6838 (tpp80) REVERT: B 329 ASP cc_start: 0.7971 (t0) cc_final: 0.7483 (m-30) REVERT: C 155 HIS cc_start: 0.7856 (t-90) cc_final: 0.6980 (t-90) REVERT: C 165 CYS cc_start: 0.8184 (t) cc_final: 0.7564 (t) REVERT: C 286 HIS cc_start: 0.7745 (t70) cc_final: 0.7240 (t70) REVERT: D 8 ASN cc_start: 0.8465 (t0) cc_final: 0.8224 (t0) REVERT: D 57 LYS cc_start: 0.7510 (ptmt) cc_final: 0.7063 (ptpp) REVERT: D 64 ASN cc_start: 0.8051 (t0) cc_final: 0.7466 (m-40) REVERT: D 119 LEU cc_start: 0.8340 (tp) cc_final: 0.8106 (tp) REVERT: D 162 ARG cc_start: 0.7772 (tpp80) cc_final: 0.7385 (ttp-170) REVERT: D 280 MET cc_start: 0.8618 (mmt) cc_final: 0.7972 (mmm) REVERT: E 61 GLU cc_start: 0.5713 (tp30) cc_final: 0.5178 (tp30) REVERT: E 79 GLU cc_start: 0.5888 (tp30) cc_final: 0.5223 (tp30) REVERT: E 83 ARG cc_start: 0.5545 (tpp80) cc_final: 0.5181 (tpp80) REVERT: E 93 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: E 97 ASN cc_start: 0.8114 (m-40) cc_final: 0.7786 (m-40) REVERT: E 98 SER cc_start: 0.8420 (t) cc_final: 0.7703 (p) REVERT: F 77 LYS cc_start: 0.7849 (tppt) cc_final: 0.7433 (tppt) REVERT: F 89 LYS cc_start: 0.7683 (tppp) cc_final: 0.7239 (ttpt) REVERT: F 137 GLU cc_start: 0.7647 (tp30) cc_final: 0.6990 (tp30) REVERT: G 27 GLU cc_start: 0.7642 (tt0) cc_final: 0.7237 (tt0) REVERT: G 82 ASP cc_start: 0.8232 (m-30) cc_final: 0.7981 (m-30) REVERT: G 117 ASN cc_start: 0.7087 (t0) cc_final: 0.6597 (p0) REVERT: G 119 GLN cc_start: 0.8571 (pp30) cc_final: 0.8214 (pm20) REVERT: G 129 TRP cc_start: 0.7934 (m100) cc_final: 0.7692 (m100) REVERT: M 100 GLU cc_start: 0.7764 (pm20) cc_final: 0.7254 (pm20) REVERT: M 122 ILE cc_start: 0.8065 (mt) cc_final: 0.7786 (mm) REVERT: M 123 MET cc_start: 0.7824 (tpp) cc_final: 0.7320 (ttm) REVERT: M 128 ASN cc_start: 0.8521 (t0) cc_final: 0.8077 (m-40) REVERT: N 44 MET cc_start: 0.5209 (tpt) cc_final: 0.4291 (mtm) REVERT: N 210 ARG cc_start: 0.8451 (tmm-80) cc_final: 0.8193 (ttp-110) REVERT: O 157 ASP cc_start: 0.8513 (t70) cc_final: 0.8073 (t0) REVERT: O 206 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7666 (ttp80) REVERT: P 69 TYR cc_start: 0.8231 (m-80) cc_final: 0.7897 (m-80) REVERT: P 89 THR cc_start: 0.8826 (m) cc_final: 0.8391 (p) REVERT: P 121 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7935 (tm-30) REVERT: P 227 MET cc_start: 0.8886 (mmm) cc_final: 0.8516 (mmt) REVERT: P 313 MET cc_start: 0.8135 (tpp) cc_final: 0.7860 (tpt) REVERT: P 316 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7803 (mm-30) REVERT: Q 47 MET cc_start: 0.7048 (mmm) cc_final: 0.5769 (ptp) REVERT: Q 59 GLN cc_start: 0.8642 (tp40) cc_final: 0.8213 (tm-30) REVERT: Q 227 MET cc_start: 0.8589 (mmm) cc_final: 0.8236 (mmm) REVERT: Q 283 MET cc_start: 0.8538 (mmm) cc_final: 0.7901 (mmp) REVERT: R 82 MET cc_start: 0.8884 (tpp) cc_final: 0.8444 (mmm) REVERT: R 137 GLN cc_start: 0.8197 (mt0) cc_final: 0.7588 (mp10) REVERT: R 269 MET cc_start: 0.8283 (ttm) cc_final: 0.7944 (ttm) REVERT: H 44 MET cc_start: 0.4535 (tpt) cc_final: 0.3875 (tpt) REVERT: H 123 MET cc_start: 0.8041 (ttm) cc_final: 0.7686 (ttm) REVERT: H 236 LEU cc_start: 0.7716 (pt) cc_final: 0.7396 (mt) REVERT: H 238 LYS cc_start: 0.7125 (mmmm) cc_final: 0.6883 (mptt) REVERT: H 249 THR cc_start: 0.8201 (m) cc_final: 0.7730 (p) REVERT: H 355 MET cc_start: 0.7363 (pmm) cc_final: 0.7128 (pmm) REVERT: H 356 TRP cc_start: 0.7239 (m100) cc_final: 0.6303 (m100) REVERT: I 59 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7777 (tp40) REVERT: I 82 MET cc_start: 0.8285 (mmt) cc_final: 0.7934 (mmm) REVERT: I 154 ASP cc_start: 0.8230 (t70) cc_final: 0.7624 (t70) REVERT: I 178 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7504 (tt) REVERT: I 207 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7587 (mm-30) REVERT: I 222 ASP cc_start: 0.6507 (OUTLIER) cc_final: 0.5989 (p0) REVERT: I 241 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7126 (tm-30) REVERT: I 280 ASN cc_start: 0.7262 (m-40) cc_final: 0.6953 (m-40) REVERT: I 296 ASN cc_start: 0.5727 (t0) cc_final: 0.5381 (t0) REVERT: I 325 MET cc_start: 0.6539 (ppp) cc_final: 0.5849 (ppp) outliers start: 145 outliers final: 103 residues processed: 708 average time/residue: 0.4968 time to fit residues: 568.3716 Evaluate side-chains 683 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 572 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 363 ASP Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 184 ASP Chi-restraints excluded: chain P residue 282 ILE Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 257 CYS Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 2.9990 chunk 424 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 276 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 472 optimal weight: 7.9990 chunk 391 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 296 ASN ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN P 12 ASN ** Q 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN R 111 ASN ** R 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS H 297 ASN I 49 GLN I 78 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.132 40028 Z= 0.488 Angle : 0.748 12.536 54326 Z= 0.374 Chirality : 0.050 0.183 6016 Planarity : 0.006 0.069 6988 Dihedral : 8.647 160.700 5545 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.11 % Favored : 93.87 % Rotamer: Outliers : 4.13 % Allowed : 18.96 % Favored : 76.92 % 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: -0.68 (0.12), residues: 4875 helix: 0.26 (0.12), residues: 1787 sheet: -0.80 (0.17), residues: 971 loop : -0.76 (0.14), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 160 HIS 0.007 0.002 HIS C 286 PHE 0.024 0.002 PHE Q 127 TYR 0.036 0.002 TYR G 112 ARG 0.008 0.001 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 576 time to evaluate : 4.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5417 (OUTLIER) cc_final: 0.4063 (m-80) REVERT: A 95 ARG cc_start: 0.7124 (ptp-170) cc_final: 0.6795 (ptp-170) REVERT: A 133 LEU cc_start: 0.7873 (mp) cc_final: 0.7232 (tp) REVERT: A 140 GLU cc_start: 0.8704 (tt0) cc_final: 0.8211 (pt0) REVERT: A 147 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8402 (m-10) REVERT: A 188 ASP cc_start: 0.8040 (t70) cc_final: 0.7791 (t0) REVERT: A 214 ARG cc_start: 0.7395 (ttt90) cc_final: 0.6873 (ttm170) REVERT: A 239 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7384 (mpt-90) REVERT: A 264 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6358 (mtt180) REVERT: A 265 TYR cc_start: 0.7157 (m-80) cc_final: 0.6549 (m-80) REVERT: A 281 ASP cc_start: 0.8257 (t0) cc_final: 0.7803 (t0) REVERT: A 368 LYS cc_start: 0.7825 (pptt) cc_final: 0.6684 (mmtm) REVERT: A 420 TYR cc_start: 0.4825 (t80) cc_final: 0.4606 (t80) REVERT: B 19 TYR cc_start: 0.7768 (m-80) cc_final: 0.7385 (m-10) REVERT: B 51 ASP cc_start: 0.6299 (t0) cc_final: 0.6046 (t0) REVERT: B 62 ARG cc_start: 0.7392 (ttp80) cc_final: 0.7184 (ttp80) REVERT: B 64 LEU cc_start: 0.8197 (mp) cc_final: 0.7968 (mt) REVERT: B 85 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8514 (tt) REVERT: B 162 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8768 (pp) REVERT: B 227 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7274 (t-90) REVERT: B 277 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7305 (t80) REVERT: B 283 GLN cc_start: 0.8144 (tp40) cc_final: 0.7576 (mm110) REVERT: B 320 LEU cc_start: 0.8166 (tp) cc_final: 0.7912 (tp) REVERT: C 155 HIS cc_start: 0.8061 (t-90) cc_final: 0.7292 (t-90) REVERT: C 165 CYS cc_start: 0.8295 (t) cc_final: 0.7632 (t) REVERT: C 286 HIS cc_start: 0.7885 (t70) cc_final: 0.7338 (t70) REVERT: D 8 ASN cc_start: 0.8553 (t0) cc_final: 0.8296 (t0) REVERT: D 57 LYS cc_start: 0.7731 (ptmt) cc_final: 0.7273 (ptpp) REVERT: D 64 ASN cc_start: 0.8369 (t0) cc_final: 0.7624 (m-40) REVERT: D 162 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7443 (ttp-170) REVERT: D 280 MET cc_start: 0.8787 (mmt) cc_final: 0.8322 (mmm) REVERT: E 22 MET cc_start: 0.4685 (tmm) cc_final: 0.4099 (tmm) REVERT: E 52 ARG cc_start: 0.6682 (ptm160) cc_final: 0.5988 (ptt180) REVERT: E 76 PHE cc_start: 0.6100 (t80) cc_final: 0.5785 (t80) REVERT: E 93 GLU cc_start: 0.7785 (mp0) cc_final: 0.7402 (mp0) REVERT: E 97 ASN cc_start: 0.8056 (m-40) cc_final: 0.7672 (m-40) REVERT: E 98 SER cc_start: 0.8396 (t) cc_final: 0.7866 (p) REVERT: F 77 LYS cc_start: 0.7946 (tppt) cc_final: 0.7613 (tppt) REVERT: F 89 LYS cc_start: 0.7634 (tppp) cc_final: 0.7319 (ttpt) REVERT: F 137 GLU cc_start: 0.7735 (tp30) cc_final: 0.6895 (tp30) REVERT: G 27 GLU cc_start: 0.7688 (tt0) cc_final: 0.7456 (tt0) REVERT: G 82 ASP cc_start: 0.8232 (m-30) cc_final: 0.7997 (m-30) REVERT: G 117 ASN cc_start: 0.7246 (t0) cc_final: 0.6515 (p0) REVERT: G 119 GLN cc_start: 0.8583 (pp30) cc_final: 0.8202 (pm20) REVERT: G 129 TRP cc_start: 0.7943 (m100) cc_final: 0.7669 (m100) REVERT: M 100 GLU cc_start: 0.7985 (pm20) cc_final: 0.7733 (pm20) REVERT: M 122 ILE cc_start: 0.8218 (mt) cc_final: 0.7956 (mm) REVERT: M 123 MET cc_start: 0.7893 (tpp) cc_final: 0.7470 (ttm) REVERT: M 128 ASN cc_start: 0.8610 (t0) cc_final: 0.8281 (m-40) REVERT: N 44 MET cc_start: 0.4400 (tpt) cc_final: 0.3698 (mtm) REVERT: N 210 ARG cc_start: 0.8452 (tmm-80) cc_final: 0.8218 (ttp-110) REVERT: O 206 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7718 (ttp80) REVERT: O 291 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8774 (ttmt) REVERT: P 64 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8626 (mp) REVERT: P 69 TYR cc_start: 0.8265 (m-80) cc_final: 0.7954 (m-80) REVERT: P 89 THR cc_start: 0.8927 (m) cc_final: 0.8538 (p) REVERT: P 227 MET cc_start: 0.8870 (mmm) cc_final: 0.8567 (mmt) REVERT: P 313 MET cc_start: 0.8195 (tpp) cc_final: 0.7955 (tpt) REVERT: Q 47 MET cc_start: 0.7338 (mmm) cc_final: 0.6073 (ptp) REVERT: Q 59 GLN cc_start: 0.8641 (tp40) cc_final: 0.8276 (tm-30) REVERT: Q 227 MET cc_start: 0.8470 (mmm) cc_final: 0.8166 (mmm) REVERT: Q 283 MET cc_start: 0.8557 (mmm) cc_final: 0.7465 (mmt) REVERT: R 184 ASP cc_start: 0.8281 (m-30) cc_final: 0.8007 (m-30) REVERT: R 276 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7747 (mt-10) REVERT: H 238 LYS cc_start: 0.7138 (mmmm) cc_final: 0.6863 (mptt) REVERT: H 260 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7863 (p) REVERT: H 355 MET cc_start: 0.7341 (pmm) cc_final: 0.7051 (pmm) REVERT: I 50 LYS cc_start: 0.8006 (mmpt) cc_final: 0.7708 (mmmt) REVERT: I 59 GLN cc_start: 0.8132 (tp-100) cc_final: 0.7779 (tp40) REVERT: I 82 MET cc_start: 0.8275 (mmt) cc_final: 0.7933 (mmm) REVERT: I 154 ASP cc_start: 0.8289 (t70) cc_final: 0.7615 (t70) REVERT: I 178 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7619 (tt) REVERT: I 207 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7451 (mm-30) REVERT: I 222 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.5918 (p0) REVERT: I 280 ASN cc_start: 0.7194 (m-40) cc_final: 0.6841 (m-40) REVERT: I 296 ASN cc_start: 0.5586 (t0) cc_final: 0.5125 (t0) REVERT: I 325 MET cc_start: 0.6598 (ppp) cc_final: 0.5972 (ppp) outliers start: 174 outliers final: 138 residues processed: 701 average time/residue: 0.5157 time to fit residues: 581.1831 Evaluate side-chains 701 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 552 time to evaluate : 4.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 20 ASP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 92 ASN Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 184 ASP Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 289 ILE Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 153 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 184 ASP Chi-restraints excluded: chain P residue 282 ILE Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 49 GLN Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain Q residue 151 ILE Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 257 CYS Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 344 optimal weight: 0.5980 chunk 267 optimal weight: 2.9990 chunk 397 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 470 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 chunk 217 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 ASN Q 275 HIS R 111 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS H 296 ASN I 49 GLN I 78 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40028 Z= 0.197 Angle : 0.619 12.170 54326 Z= 0.304 Chirality : 0.045 0.191 6016 Planarity : 0.004 0.062 6988 Dihedral : 8.100 157.586 5545 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.13 % Allowed : 20.69 % Favored : 76.18 % 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: -0.31 (0.12), residues: 4875 helix: 0.55 (0.12), residues: 1796 sheet: -0.64 (0.17), residues: 963 loop : -0.51 (0.14), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 340 HIS 0.006 0.001 HIS C 286 PHE 0.024 0.001 PHE A 150 TYR 0.023 0.001 TYR G 112 ARG 0.007 0.000 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 600 time to evaluate : 4.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5280 (OUTLIER) cc_final: 0.3942 (m-80) REVERT: A 83 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7432 (ttmm) REVERT: A 95 ARG cc_start: 0.7161 (ptp-170) cc_final: 0.6863 (ptp-170) REVERT: A 101 ASN cc_start: 0.6589 (t0) cc_final: 0.6338 (t0) REVERT: A 133 LEU cc_start: 0.7674 (mp) cc_final: 0.7080 (tp) REVERT: A 140 GLU cc_start: 0.8619 (tt0) cc_final: 0.8190 (pt0) REVERT: A 188 ASP cc_start: 0.7872 (t70) cc_final: 0.7656 (t0) REVERT: A 194 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8681 (mm) REVERT: A 214 ARG cc_start: 0.7111 (ttt90) cc_final: 0.6565 (ttm170) REVERT: A 239 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7536 (mpt90) REVERT: A 265 TYR cc_start: 0.7257 (m-80) cc_final: 0.6731 (m-80) REVERT: A 281 ASP cc_start: 0.8266 (t0) cc_final: 0.7818 (t0) REVERT: A 368 LYS cc_start: 0.7766 (pptt) cc_final: 0.6670 (mmtm) REVERT: B 19 TYR cc_start: 0.7708 (m-80) cc_final: 0.7329 (m-10) REVERT: B 51 ASP cc_start: 0.6231 (t0) cc_final: 0.6023 (t0) REVERT: B 64 LEU cc_start: 0.8078 (mp) cc_final: 0.7839 (mt) REVERT: B 85 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8467 (tt) REVERT: B 227 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7120 (t-90) REVERT: B 320 LEU cc_start: 0.8067 (tp) cc_final: 0.7740 (tp) REVERT: B 361 MET cc_start: 0.7722 (ptm) cc_final: 0.7262 (ttp) REVERT: C 155 HIS cc_start: 0.8038 (t-90) cc_final: 0.7272 (t-90) REVERT: C 165 CYS cc_start: 0.8215 (t) cc_final: 0.7579 (t) REVERT: C 286 HIS cc_start: 0.7886 (t70) cc_final: 0.7461 (t70) REVERT: D 8 ASN cc_start: 0.8469 (t0) cc_final: 0.8197 (t0) REVERT: D 57 LYS cc_start: 0.7610 (ptmt) cc_final: 0.7068 (ptpp) REVERT: D 64 ASN cc_start: 0.8372 (t0) cc_final: 0.7828 (m-40) REVERT: D 280 MET cc_start: 0.8595 (mmm) cc_final: 0.8184 (mmp) REVERT: E 22 MET cc_start: 0.4705 (OUTLIER) cc_final: 0.4104 (tmm) REVERT: E 59 ASN cc_start: 0.7208 (t0) cc_final: 0.6999 (t0) REVERT: E 61 GLU cc_start: 0.5575 (tp30) cc_final: 0.5145 (tp30) REVERT: E 76 PHE cc_start: 0.6012 (t80) cc_final: 0.5698 (t80) REVERT: E 97 ASN cc_start: 0.8071 (m-40) cc_final: 0.7747 (m-40) REVERT: E 98 SER cc_start: 0.8386 (t) cc_final: 0.7772 (p) REVERT: F 77 LYS cc_start: 0.7946 (tppt) cc_final: 0.7579 (tppt) REVERT: F 89 LYS cc_start: 0.7758 (tppp) cc_final: 0.7262 (ttpt) REVERT: F 119 THR cc_start: 0.8939 (m) cc_final: 0.8420 (p) REVERT: F 137 GLU cc_start: 0.7637 (tp30) cc_final: 0.7125 (tp30) REVERT: G 27 GLU cc_start: 0.7731 (tt0) cc_final: 0.7458 (tt0) REVERT: G 82 ASP cc_start: 0.8246 (m-30) cc_final: 0.8032 (m-30) REVERT: G 117 ASN cc_start: 0.7169 (t0) cc_final: 0.6538 (p0) REVERT: G 119 GLN cc_start: 0.8598 (pp30) cc_final: 0.8214 (pm20) REVERT: G 129 TRP cc_start: 0.7783 (m100) cc_final: 0.7528 (m100) REVERT: M 100 GLU cc_start: 0.8004 (pm20) cc_final: 0.7733 (pm20) REVERT: M 122 ILE cc_start: 0.8196 (mt) cc_final: 0.7917 (mm) REVERT: M 128 ASN cc_start: 0.8611 (t0) cc_final: 0.8267 (m-40) REVERT: N 44 MET cc_start: 0.4794 (tpt) cc_final: 0.3970 (mtm) REVERT: N 94 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8430 (mm) REVERT: N 288 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: O 206 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7669 (ttp80) REVERT: O 291 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8748 (ttmt) REVERT: P 64 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8532 (mp) REVERT: P 68 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8102 (mtpp) REVERT: P 69 TYR cc_start: 0.8146 (m-80) cc_final: 0.7864 (m-80) REVERT: P 89 THR cc_start: 0.8719 (m) cc_final: 0.8404 (p) REVERT: P 227 MET cc_start: 0.8856 (mmm) cc_final: 0.8523 (mmt) REVERT: P 325 MET cc_start: 0.7810 (ptp) cc_final: 0.7461 (ptm) REVERT: Q 47 MET cc_start: 0.7049 (mmm) cc_final: 0.5827 (ptp) REVERT: Q 59 GLN cc_start: 0.8615 (tp40) cc_final: 0.8327 (tm-30) REVERT: Q 176 MET cc_start: 0.8307 (mmm) cc_final: 0.8093 (mmt) REVERT: Q 227 MET cc_start: 0.8470 (mmm) cc_final: 0.8076 (mmm) REVERT: Q 283 MET cc_start: 0.8579 (mmm) cc_final: 0.7518 (mmt) REVERT: R 82 MET cc_start: 0.8710 (tpp) cc_final: 0.8209 (mmm) REVERT: R 94 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7597 (mp) REVERT: R 184 ASP cc_start: 0.8141 (m-30) cc_final: 0.7901 (m-30) REVERT: R 276 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7790 (mt-10) REVERT: H 325 MET cc_start: 0.7883 (mmt) cc_final: 0.7528 (mmt) REVERT: H 355 MET cc_start: 0.7196 (pmm) cc_final: 0.6983 (pmm) REVERT: H 356 TRP cc_start: 0.7243 (m100) cc_final: 0.6294 (m100) REVERT: I 50 LYS cc_start: 0.7966 (mmpt) cc_final: 0.7681 (mmmt) REVERT: I 59 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7673 (tp40) REVERT: I 82 MET cc_start: 0.8143 (mmt) cc_final: 0.7837 (mmm) REVERT: I 154 ASP cc_start: 0.8063 (t70) cc_final: 0.7391 (t70) REVERT: I 207 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7492 (mm-30) REVERT: I 222 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.6034 (p0) REVERT: I 280 ASN cc_start: 0.7238 (m-40) cc_final: 0.6872 (m-40) REVERT: I 296 ASN cc_start: 0.5672 (t0) cc_final: 0.5245 (t0) REVERT: I 325 MET cc_start: 0.6257 (ppp) cc_final: 0.5810 (ppp) outliers start: 132 outliers final: 88 residues processed: 693 average time/residue: 0.5107 time to fit residues: 568.8727 Evaluate side-chains 665 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 566 time to evaluate : 4.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 288 ASP Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 257 CYS Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 119 MET Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 277 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 299 MET Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 280 optimal weight: 0.0070 chunk 141 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 299 optimal weight: 0.9980 chunk 320 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 369 optimal weight: 6.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS H 296 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN I 173 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 40028 Z= 0.159 Angle : 0.604 15.720 54326 Z= 0.292 Chirality : 0.044 0.187 6016 Planarity : 0.004 0.054 6988 Dihedral : 7.763 156.329 5545 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.54 % Allowed : 21.52 % Favored : 75.94 % 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: -0.11 (0.12), residues: 4875 helix: 0.70 (0.12), residues: 1786 sheet: -0.54 (0.17), residues: 962 loop : -0.37 (0.14), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 340 HIS 0.006 0.001 HIS C 286 PHE 0.018 0.001 PHE D 127 TYR 0.023 0.001 TYR I 218 ARG 0.010 0.000 ARG E 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 611 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5044 (OUTLIER) cc_final: 0.3751 (m-80) REVERT: A 83 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7614 (ttmm) REVERT: A 100 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: A 101 ASN cc_start: 0.6676 (t0) cc_final: 0.6445 (t0) REVERT: A 133 LEU cc_start: 0.7602 (mp) cc_final: 0.7027 (tp) REVERT: A 140 GLU cc_start: 0.8548 (tt0) cc_final: 0.7993 (pt0) REVERT: A 194 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8676 (mm) REVERT: A 214 ARG cc_start: 0.7078 (ttt90) cc_final: 0.6622 (ttm170) REVERT: A 239 ARG cc_start: 0.7919 (mmt-90) cc_final: 0.7444 (mpt-90) REVERT: A 265 TYR cc_start: 0.7057 (m-80) cc_final: 0.6481 (m-80) REVERT: A 281 ASP cc_start: 0.8237 (t0) cc_final: 0.7667 (t0) REVERT: A 368 LYS cc_start: 0.7746 (pptt) cc_final: 0.6666 (mmtm) REVERT: B 19 TYR cc_start: 0.7731 (m-80) cc_final: 0.7223 (m-10) REVERT: B 51 ASP cc_start: 0.6245 (t0) cc_final: 0.6031 (t0) REVERT: B 54 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.7352 (p) REVERT: B 64 LEU cc_start: 0.8161 (mp) cc_final: 0.7910 (mt) REVERT: B 227 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7158 (t-90) REVERT: B 283 GLN cc_start: 0.7939 (tp40) cc_final: 0.7428 (mm110) REVERT: B 320 LEU cc_start: 0.8052 (tp) cc_final: 0.7735 (tp) REVERT: B 361 MET cc_start: 0.7683 (ptm) cc_final: 0.7209 (ttp) REVERT: C 75 GLN cc_start: 0.7401 (tt0) cc_final: 0.7118 (tt0) REVERT: C 155 HIS cc_start: 0.7817 (t-90) cc_final: 0.7035 (t-90) REVERT: C 165 CYS cc_start: 0.7989 (t) cc_final: 0.7451 (t) REVERT: C 286 HIS cc_start: 0.7788 (t70) cc_final: 0.7226 (t70) REVERT: D 5 ASP cc_start: 0.7447 (t0) cc_final: 0.7195 (m-30) REVERT: D 8 ASN cc_start: 0.8430 (t0) cc_final: 0.8141 (t0) REVERT: D 57 LYS cc_start: 0.7576 (ptmt) cc_final: 0.7108 (ptpp) REVERT: D 64 ASN cc_start: 0.8088 (t0) cc_final: 0.7638 (m-40) REVERT: D 186 GLU cc_start: 0.7287 (tp30) cc_final: 0.7032 (tp30) REVERT: E 76 PHE cc_start: 0.5949 (t80) cc_final: 0.5618 (t80) REVERT: E 93 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: E 97 ASN cc_start: 0.8170 (m-40) cc_final: 0.7778 (m-40) REVERT: E 98 SER cc_start: 0.8375 (t) cc_final: 0.7753 (p) REVERT: F 77 LYS cc_start: 0.7816 (tppt) cc_final: 0.7538 (tppt) REVERT: F 89 LYS cc_start: 0.7626 (tppp) cc_final: 0.7030 (tppt) REVERT: G 27 GLU cc_start: 0.7771 (tt0) cc_final: 0.7510 (tp30) REVERT: G 75 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8084 (mm-40) REVERT: G 117 ASN cc_start: 0.7128 (t0) cc_final: 0.6528 (p0) REVERT: G 119 GLN cc_start: 0.8537 (pp30) cc_final: 0.8097 (pm20) REVERT: G 129 TRP cc_start: 0.7778 (m100) cc_final: 0.7541 (m100) REVERT: M 100 GLU cc_start: 0.7973 (pm20) cc_final: 0.7695 (pm20) REVERT: M 122 ILE cc_start: 0.8219 (mt) cc_final: 0.7932 (mm) REVERT: M 128 ASN cc_start: 0.8507 (t0) cc_final: 0.8217 (m-40) REVERT: M 325 MET cc_start: 0.7324 (ptm) cc_final: 0.7023 (ptm) REVERT: N 44 MET cc_start: 0.5099 (tpt) cc_final: 0.4106 (mtm) REVERT: O 206 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7633 (ttp80) REVERT: O 283 MET cc_start: 0.8659 (mmm) cc_final: 0.8426 (mmm) REVERT: O 291 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8638 (ttmt) REVERT: P 47 MET cc_start: 0.7394 (pmm) cc_final: 0.6526 (pmm) REVERT: P 69 TYR cc_start: 0.8195 (m-80) cc_final: 0.7950 (m-80) REVERT: P 89 THR cc_start: 0.8690 (m) cc_final: 0.8387 (p) REVERT: P 227 MET cc_start: 0.8887 (mmm) cc_final: 0.8566 (mmt) REVERT: Q 17 VAL cc_start: 0.9016 (m) cc_final: 0.8798 (p) REVERT: Q 47 MET cc_start: 0.7168 (mmm) cc_final: 0.5891 (ptp) REVERT: Q 59 GLN cc_start: 0.8601 (tp40) cc_final: 0.8314 (tm-30) REVERT: Q 176 MET cc_start: 0.8238 (mmm) cc_final: 0.8020 (mmt) REVERT: Q 227 MET cc_start: 0.8317 (mmm) cc_final: 0.7889 (mmm) REVERT: Q 283 MET cc_start: 0.8604 (mmm) cc_final: 0.7476 (mmt) REVERT: Q 346 LEU cc_start: 0.9060 (tp) cc_final: 0.8834 (tp) REVERT: R 82 MET cc_start: 0.8752 (tpp) cc_final: 0.8331 (mmm) REVERT: R 276 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7811 (mt-10) REVERT: H 236 LEU cc_start: 0.7625 (pt) cc_final: 0.7346 (mt) REVERT: H 260 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7886 (p) REVERT: H 313 MET cc_start: 0.8245 (tpt) cc_final: 0.7843 (tpp) REVERT: H 325 MET cc_start: 0.7972 (mmt) cc_final: 0.7595 (mmt) REVERT: I 50 LYS cc_start: 0.7954 (mmpt) cc_final: 0.7666 (mmmt) REVERT: I 59 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7678 (tp40) REVERT: I 82 MET cc_start: 0.8250 (mmt) cc_final: 0.7943 (mmm) REVERT: I 120 THR cc_start: 0.7418 (m) cc_final: 0.7198 (p) REVERT: I 154 ASP cc_start: 0.7958 (t70) cc_final: 0.7273 (t70) REVERT: I 207 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7468 (mm-30) REVERT: I 222 ASP cc_start: 0.6271 (OUTLIER) cc_final: 0.5881 (p0) REVERT: I 241 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7156 (tm-30) REVERT: I 280 ASN cc_start: 0.7264 (m-40) cc_final: 0.6918 (m-40) REVERT: I 294 TYR cc_start: 0.7415 (m-10) cc_final: 0.7139 (m-10) REVERT: I 296 ASN cc_start: 0.5672 (t0) cc_final: 0.5204 (t0) REVERT: I 325 MET cc_start: 0.6238 (ppp) cc_final: 0.5783 (ppp) outliers start: 107 outliers final: 73 residues processed: 686 average time/residue: 0.5279 time to fit residues: 583.4088 Evaluate side-chains 656 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 575 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 205 GLU Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 257 CYS Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 173 HIS Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 0.9980 chunk 450 optimal weight: 0.0070 chunk 411 optimal weight: 8.9990 chunk 438 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 344 optimal weight: 5.9990 chunk 134 optimal weight: 0.0050 chunk 396 optimal weight: 2.9990 chunk 414 optimal weight: 2.9990 chunk 436 optimal weight: 3.9990 overall best weight: 1.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 ASN Q 115 ASN ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS H 296 ASN I 49 GLN I 78 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40028 Z= 0.200 Angle : 0.616 15.937 54326 Z= 0.299 Chirality : 0.044 0.230 6016 Planarity : 0.004 0.065 6988 Dihedral : 7.688 157.064 5545 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.51 % Allowed : 21.90 % Favored : 75.59 % 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: -0.07 (0.12), residues: 4875 helix: 0.70 (0.12), residues: 1786 sheet: -0.46 (0.17), residues: 968 loop : -0.34 (0.15), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 340 HIS 0.028 0.001 HIS I 173 PHE 0.023 0.001 PHE B 24 TYR 0.025 0.001 TYR I 218 ARG 0.009 0.000 ARG E 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 588 time to evaluate : 4.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.5066 (OUTLIER) cc_final: 0.3776 (m-80) REVERT: A 83 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7636 (ttmm) REVERT: A 101 ASN cc_start: 0.6707 (t0) cc_final: 0.6494 (t0) REVERT: A 133 LEU cc_start: 0.7687 (mp) cc_final: 0.7106 (tp) REVERT: A 194 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8677 (mm) REVERT: A 214 ARG cc_start: 0.7014 (ttt90) cc_final: 0.6632 (ttm170) REVERT: A 239 ARG cc_start: 0.7798 (mmt-90) cc_final: 0.7523 (mpt90) REVERT: A 265 TYR cc_start: 0.7345 (m-80) cc_final: 0.6870 (m-80) REVERT: A 266 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7189 (mm) REVERT: A 281 ASP cc_start: 0.8262 (t0) cc_final: 0.7707 (t0) REVERT: A 368 LYS cc_start: 0.7780 (pptt) cc_final: 0.6695 (mmtm) REVERT: B 19 TYR cc_start: 0.7658 (m-80) cc_final: 0.7180 (m-10) REVERT: B 51 ASP cc_start: 0.6266 (t0) cc_final: 0.6062 (t0) REVERT: B 54 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7393 (p) REVERT: B 227 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7109 (t-90) REVERT: B 283 GLN cc_start: 0.7959 (tp40) cc_final: 0.7448 (mm110) REVERT: B 319 GLN cc_start: 0.7545 (pt0) cc_final: 0.7343 (pt0) REVERT: B 320 LEU cc_start: 0.8040 (tp) cc_final: 0.7746 (tp) REVERT: B 361 MET cc_start: 0.7599 (ptm) cc_final: 0.7314 (ttp) REVERT: C 155 HIS cc_start: 0.7849 (t-90) cc_final: 0.7037 (t-90) REVERT: C 165 CYS cc_start: 0.7985 (t) cc_final: 0.7435 (t) REVERT: C 286 HIS cc_start: 0.7765 (t70) cc_final: 0.7226 (t70) REVERT: D 5 ASP cc_start: 0.7482 (t0) cc_final: 0.7211 (m-30) REVERT: D 8 ASN cc_start: 0.8417 (t0) cc_final: 0.8135 (t0) REVERT: D 57 LYS cc_start: 0.7599 (ptmt) cc_final: 0.7125 (ptpp) REVERT: D 64 ASN cc_start: 0.8109 (t0) cc_final: 0.7636 (m-40) REVERT: D 229 ILE cc_start: 0.7428 (mm) cc_final: 0.6975 (mp) REVERT: E 76 PHE cc_start: 0.5975 (t80) cc_final: 0.5639 (t80) REVERT: E 97 ASN cc_start: 0.8150 (m-40) cc_final: 0.7761 (m-40) REVERT: E 98 SER cc_start: 0.8409 (t) cc_final: 0.7756 (p) REVERT: F 77 LYS cc_start: 0.7837 (tppt) cc_final: 0.7541 (tppt) REVERT: F 89 LYS cc_start: 0.7538 (tppp) cc_final: 0.7228 (ttpt) REVERT: G 27 GLU cc_start: 0.7731 (tt0) cc_final: 0.7439 (tp30) REVERT: G 75 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8092 (mm-40) REVERT: G 117 ASN cc_start: 0.7120 (t0) cc_final: 0.6523 (p0) REVERT: G 119 GLN cc_start: 0.8604 (pp30) cc_final: 0.8124 (pm20) REVERT: G 129 TRP cc_start: 0.7786 (m100) cc_final: 0.7523 (m100) REVERT: M 28 ARG cc_start: 0.6746 (mtp-110) cc_final: 0.6032 (ttt-90) REVERT: M 100 GLU cc_start: 0.7995 (pm20) cc_final: 0.7715 (pm20) REVERT: M 122 ILE cc_start: 0.8228 (mt) cc_final: 0.7953 (mm) REVERT: M 124 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: M 128 ASN cc_start: 0.8563 (t0) cc_final: 0.8273 (m-40) REVERT: M 325 MET cc_start: 0.7275 (ptm) cc_final: 0.6947 (ptm) REVERT: N 44 MET cc_start: 0.5087 (tpt) cc_final: 0.4103 (mtm) REVERT: N 288 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: O 206 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7649 (ttp80) REVERT: O 291 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8641 (ttmt) REVERT: P 47 MET cc_start: 0.7429 (pmm) cc_final: 0.6571 (pmm) REVERT: P 69 TYR cc_start: 0.8174 (m-80) cc_final: 0.7868 (m-80) REVERT: P 89 THR cc_start: 0.8711 (m) cc_final: 0.8410 (p) REVERT: P 227 MET cc_start: 0.8878 (mmm) cc_final: 0.8556 (mmt) REVERT: P 316 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7636 (mm-30) REVERT: P 325 MET cc_start: 0.7792 (ptp) cc_final: 0.7485 (ptm) REVERT: Q 17 VAL cc_start: 0.9011 (m) cc_final: 0.8780 (p) REVERT: Q 47 MET cc_start: 0.7179 (mmm) cc_final: 0.5881 (ptp) REVERT: Q 59 GLN cc_start: 0.8601 (tp40) cc_final: 0.8324 (tm-30) REVERT: Q 227 MET cc_start: 0.8328 (mmm) cc_final: 0.7910 (mmm) REVERT: Q 283 MET cc_start: 0.8617 (mmm) cc_final: 0.7495 (mmt) REVERT: R 82 MET cc_start: 0.8726 (tpp) cc_final: 0.8361 (mmm) REVERT: R 276 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7798 (mt-10) REVERT: H 237 GLU cc_start: 0.7704 (mt-10) cc_final: 0.6908 (pm20) REVERT: H 260 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.7880 (p) REVERT: H 286 ASP cc_start: 0.7436 (p0) cc_final: 0.6410 (p0) REVERT: H 290 ARG cc_start: 0.7461 (mtm180) cc_final: 0.6780 (mtm180) REVERT: H 313 MET cc_start: 0.8243 (tpt) cc_final: 0.7837 (tpp) REVERT: I 50 LYS cc_start: 0.8124 (mmpt) cc_final: 0.7789 (mmmt) REVERT: I 120 THR cc_start: 0.7426 (m) cc_final: 0.7221 (p) REVERT: I 207 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7644 (mm-30) REVERT: I 222 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5898 (p0) REVERT: I 241 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7205 (tm-30) REVERT: I 280 ASN cc_start: 0.7269 (m-40) cc_final: 0.6965 (m-40) REVERT: I 294 TYR cc_start: 0.7460 (m-10) cc_final: 0.7164 (m-10) REVERT: I 296 ASN cc_start: 0.5706 (t0) cc_final: 0.5279 (t0) REVERT: I 314 GLN cc_start: 0.6675 (tp40) cc_final: 0.6376 (tp-100) REVERT: I 325 MET cc_start: 0.6234 (ppp) cc_final: 0.5807 (ppp) outliers start: 106 outliers final: 83 residues processed: 663 average time/residue: 0.5299 time to fit residues: 567.1868 Evaluate side-chains 672 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 580 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 124 PHE Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 324 THR Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 167 GLU Chi-restraints excluded: chain N residue 205 GLU Chi-restraints excluded: chain N residue 288 ASP Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 186 THR Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Q residue 257 CYS Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 0.0070 chunk 463 optimal weight: 4.9990 chunk 282 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 322 optimal weight: 0.7980 chunk 486 optimal weight: 4.9990 chunk 447 optimal weight: 4.9990 chunk 387 optimal weight: 3.9990 chunk 40 optimal weight: 0.0770 chunk 299 optimal weight: 0.1980 chunk 237 optimal weight: 3.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** D 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN M 314 GLN ** N 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 HIS H 296 ASN I 59 GLN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 40028 Z= 0.156 Angle : 0.608 15.901 54326 Z= 0.293 Chirality : 0.044 0.234 6016 Planarity : 0.004 0.061 6988 Dihedral : 7.427 156.254 5545 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.23 % Allowed : 22.37 % Favored : 75.40 % 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: 0.04 (0.13), residues: 4875 helix: 0.77 (0.13), residues: 1782 sheet: -0.37 (0.17), residues: 968 loop : -0.28 (0.15), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 340 HIS 0.006 0.001 HIS C 286 PHE 0.019 0.001 PHE D 250 TYR 0.025 0.001 TYR I 218 ARG 0.010 0.001 ARG D 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 598 time to evaluate : 4.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.4953 (OUTLIER) cc_final: 0.3701 (m-80) REVERT: A 83 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7641 (ttmm) REVERT: A 133 LEU cc_start: 0.7783 (mp) cc_final: 0.7190 (tp) REVERT: A 140 GLU cc_start: 0.8330 (pt0) cc_final: 0.8061 (pt0) REVERT: A 194 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8678 (mm) REVERT: A 214 ARG cc_start: 0.6934 (ttt90) cc_final: 0.6607 (ttm170) REVERT: A 239 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7541 (mpt-90) REVERT: A 266 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7207 (mm) REVERT: A 281 ASP cc_start: 0.8245 (t0) cc_final: 0.7694 (t0) REVERT: A 368 LYS cc_start: 0.7750 (pptt) cc_final: 0.6687 (mmtm) REVERT: B 19 TYR cc_start: 0.7624 (m-80) cc_final: 0.7152 (m-10) REVERT: B 227 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7139 (t-90) REVERT: B 283 GLN cc_start: 0.7893 (tp40) cc_final: 0.7474 (mm110) REVERT: B 320 LEU cc_start: 0.8010 (tp) cc_final: 0.7663 (tp) REVERT: B 321 TRP cc_start: 0.8863 (t60) cc_final: 0.8195 (t60) REVERT: C 155 HIS cc_start: 0.7742 (t-90) cc_final: 0.6936 (t70) REVERT: C 165 CYS cc_start: 0.7917 (t) cc_final: 0.7406 (t) REVERT: C 286 HIS cc_start: 0.7725 (t70) cc_final: 0.7221 (t70) REVERT: D 5 ASP cc_start: 0.7456 (t0) cc_final: 0.7180 (m-30) REVERT: D 8 ASN cc_start: 0.8365 (t0) cc_final: 0.8105 (t0) REVERT: D 57 LYS cc_start: 0.7600 (ptmt) cc_final: 0.7085 (ptpp) REVERT: D 64 ASN cc_start: 0.8085 (t0) cc_final: 0.7612 (m-40) REVERT: D 113 MET cc_start: 0.7391 (tpp) cc_final: 0.6781 (mmt) REVERT: D 129 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7645 (mmtp) REVERT: D 229 ILE cc_start: 0.7486 (mm) cc_final: 0.7001 (mp) REVERT: E 76 PHE cc_start: 0.5916 (t80) cc_final: 0.5585 (t80) REVERT: E 97 ASN cc_start: 0.8113 (m-40) cc_final: 0.7731 (m-40) REVERT: E 98 SER cc_start: 0.8411 (t) cc_final: 0.7725 (p) REVERT: E 144 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7522 (mmm160) REVERT: F 25 PHE cc_start: 0.7712 (t80) cc_final: 0.7445 (t80) REVERT: F 77 LYS cc_start: 0.7868 (tppt) cc_final: 0.7525 (tppt) REVERT: F 89 LYS cc_start: 0.7755 (tppp) cc_final: 0.7246 (tppt) REVERT: G 27 GLU cc_start: 0.7690 (tt0) cc_final: 0.7364 (tp30) REVERT: G 75 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8140 (mm-40) REVERT: G 88 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7766 (tmm-80) REVERT: G 117 ASN cc_start: 0.7289 (t0) cc_final: 0.6818 (p0) REVERT: G 119 GLN cc_start: 0.8627 (pp30) cc_final: 0.8136 (pm20) REVERT: M 28 ARG cc_start: 0.6702 (mtp-110) cc_final: 0.6042 (ttt-90) REVERT: M 100 GLU cc_start: 0.8031 (pm20) cc_final: 0.7692 (pm20) REVERT: M 122 ILE cc_start: 0.8205 (mt) cc_final: 0.7913 (mm) REVERT: M 325 MET cc_start: 0.7324 (ptm) cc_final: 0.7021 (ptm) REVERT: N 44 MET cc_start: 0.5033 (tpt) cc_final: 0.4083 (mtm) REVERT: N 288 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: O 157 ASP cc_start: 0.8394 (t70) cc_final: 0.7859 (t0) REVERT: O 206 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7643 (ttp80) REVERT: O 283 MET cc_start: 0.8656 (mmm) cc_final: 0.8416 (mmm) REVERT: P 47 MET cc_start: 0.7366 (pmm) cc_final: 0.6527 (pmm) REVERT: P 69 TYR cc_start: 0.8141 (m-80) cc_final: 0.7840 (m-80) REVERT: P 89 THR cc_start: 0.8687 (m) cc_final: 0.8376 (p) REVERT: P 227 MET cc_start: 0.8873 (mmm) cc_final: 0.8553 (mmt) REVERT: P 316 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7463 (mm-30) REVERT: Q 47 MET cc_start: 0.7105 (mmm) cc_final: 0.5710 (ptp) REVERT: Q 59 GLN cc_start: 0.8571 (tp40) cc_final: 0.8240 (tm-30) REVERT: Q 106 THR cc_start: 0.8934 (m) cc_final: 0.8713 (p) REVERT: Q 176 MET cc_start: 0.8229 (mmm) cc_final: 0.8000 (mmt) REVERT: Q 227 MET cc_start: 0.8308 (mmm) cc_final: 0.7878 (mmm) REVERT: Q 283 MET cc_start: 0.8619 (mmm) cc_final: 0.8031 (mmp) REVERT: Q 346 LEU cc_start: 0.9017 (tp) cc_final: 0.8810 (tp) REVERT: R 82 MET cc_start: 0.8731 (tpp) cc_final: 0.8379 (mmm) REVERT: R 137 GLN cc_start: 0.8137 (mt0) cc_final: 0.7848 (mt0) REVERT: R 276 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7639 (mt-10) REVERT: H 237 GLU cc_start: 0.7686 (mt-10) cc_final: 0.6966 (pm20) REVERT: H 260 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7870 (p) REVERT: H 313 MET cc_start: 0.8229 (tpt) cc_final: 0.7835 (tpp) REVERT: I 50 LYS cc_start: 0.8104 (mmpt) cc_final: 0.7786 (mmmt) REVERT: I 59 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7673 (tp40) REVERT: I 82 MET cc_start: 0.8018 (mmt) cc_final: 0.7693 (mmm) REVERT: I 120 THR cc_start: 0.7407 (m) cc_final: 0.7204 (p) REVERT: I 207 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7583 (mm-30) REVERT: I 222 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6170 (p0) REVERT: I 241 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7240 (tm-30) REVERT: I 280 ASN cc_start: 0.7350 (m-40) cc_final: 0.7098 (m110) REVERT: I 294 TYR cc_start: 0.7347 (m-10) cc_final: 0.7038 (m-10) REVERT: I 296 ASN cc_start: 0.5971 (t0) cc_final: 0.5591 (t0) REVERT: I 314 GLN cc_start: 0.6764 (tp40) cc_final: 0.6482 (tp-100) REVERT: I 325 MET cc_start: 0.6208 (ppp) cc_final: 0.5781 (ppp) outliers start: 94 outliers final: 74 residues processed: 664 average time/residue: 0.5097 time to fit residues: 546.7832 Evaluate side-chains 653 residues out of total 4219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 572 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 160 HIS Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 GLN Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 202 THR Chi-restraints excluded: chain M residue 242 LEU Chi-restraints excluded: chain M residue 327 ILE Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 205 GLU Chi-restraints excluded: chain N residue 288 ASP Chi-restraints excluded: chain N residue 296 ASN Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 129 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 153 LEU Chi-restraints excluded: chain P residue 303 THR Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 257 CYS Chi-restraints excluded: chain Q residue 330 ILE Chi-restraints excluded: chain Q residue 338 SER Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 115 ASN Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 346 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1674 > 50: distance: 3 - 58: 12.822 distance: 14 - 61: 16.819 distance: 46 - 51: 5.006 distance: 51 - 52: 5.828 distance: 52 - 53: 10.308 distance: 52 - 55: 8.811 distance: 53 - 54: 10.801 distance: 53 - 58: 10.314 distance: 54 - 172: 16.942 distance: 55 - 56: 8.157 distance: 55 - 57: 6.546 distance: 58 - 59: 4.819 distance: 59 - 60: 8.986 distance: 59 - 62: 12.186 distance: 60 - 61: 17.752 distance: 60 - 66: 8.922 distance: 63 - 64: 11.183 distance: 63 - 65: 9.393 distance: 66 - 67: 17.819 distance: 66 - 175: 15.150 distance: 67 - 68: 19.358 distance: 67 - 70: 13.117 distance: 68 - 69: 15.904 distance: 68 - 74: 14.476 distance: 69 - 186: 24.393 distance: 70 - 71: 7.048 distance: 71 - 72: 29.103 distance: 71 - 73: 14.567 distance: 74 - 75: 15.125 distance: 75 - 76: 10.627 distance: 75 - 78: 16.621 distance: 76 - 77: 9.627 distance: 76 - 81: 11.039 distance: 78 - 79: 13.957 distance: 78 - 80: 29.262 distance: 81 - 82: 16.445 distance: 81 - 189: 19.040 distance: 82 - 83: 13.090 distance: 82 - 85: 20.476 distance: 83 - 84: 10.713 distance: 83 - 90: 18.067 distance: 85 - 86: 18.536 distance: 86 - 87: 32.183 distance: 87 - 88: 15.288 distance: 87 - 89: 28.766 distance: 90 - 91: 16.375 distance: 91 - 92: 17.023 distance: 91 - 94: 15.855 distance: 92 - 93: 16.826 distance: 92 - 95: 8.137 distance: 95 - 96: 21.329 distance: 95 - 101: 20.105 distance: 96 - 97: 29.218 distance: 96 - 99: 29.557 distance: 97 - 98: 12.993 distance: 97 - 102: 44.707 distance: 99 - 100: 12.768 distance: 100 - 101: 9.420 distance: 102 - 103: 10.973 distance: 103 - 104: 22.040 distance: 103 - 106: 18.016 distance: 104 - 105: 35.102 distance: 104 - 110: 13.118 distance: 106 - 107: 13.665 distance: 107 - 108: 16.666 distance: 107 - 109: 15.276 distance: 110 - 111: 8.222 distance: 111 - 112: 22.258 distance: 111 - 114: 23.299 distance: 112 - 113: 16.988 distance: 112 - 118: 32.024 distance: 114 - 115: 19.919 distance: 115 - 116: 4.848 distance: 115 - 117: 42.582 distance: 118 - 119: 34.486 distance: 118 - 124: 16.888 distance: 119 - 120: 27.694 distance: 119 - 122: 36.702 distance: 120 - 121: 19.291 distance: 120 - 125: 17.693 distance: 122 - 123: 34.636 distance: 123 - 124: 18.791