Starting phenix.real_space_refine on Tue Mar 12 02:54:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/03_2024/6fo0_4286_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/03_2024/6fo0_4286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/03_2024/6fo0_4286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/03_2024/6fo0_4286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/03_2024/6fo0_4286_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fo0_4286/03_2024/6fo0_4286_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.035 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: 8 Type Number sf(0) Gaussians Fe 6 7.16 5 S 152 5.16 5 Cl 2 4.86 5 C 19850 2.51 5 N 5304 2.21 5 O 5674 1.98 5 F 6 1.80 5 H 30362 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 61356 Number of models: 1 Model: "" Number of chains: 24 Chain: "N" Number of atoms: 6753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6753 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "O" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6206 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 14, 'TRANS': 399} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 5933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5933 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "Q" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3751 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, 'TRANS': 216} Chain: "R" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2658 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1710 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "T" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1255 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain: "U" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1041 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "V" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 263 Classifications: {'peptide': 17} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "W" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 950 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "A" Number of atoms: 6753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 6753 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6206 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 14, 'TRANS': 399} Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5933 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "D" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3751 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, 'TRANS': 216} Chain: "E" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2658 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1710 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "G" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1255 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1041 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "I" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 263 Classifications: {'peptide': 17} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "J" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 950 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "P" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 115 Unusual residues: {'G8U': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 115 Unusual residues: {'G8U': 1, 'HEM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.60, per 1000 atoms: 0.32 Number of scatterers: 61356 At special positions: 0 Unit cell: (125.67, 137.385, 169.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 6 26.01 Cl 2 17.00 S 152 16.00 F 6 9.00 O 5674 8.00 N 5304 7.00 C 19850 6.00 H 30362 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 139 " - pdb=" SG CYS R 158 " distance=2.04 Simple disulfide: pdb=" SG CYS U 24 " - pdb=" SG CYS U 68 " distance=2.03 Simple disulfide: pdb=" SG CYS U 40 " - pdb=" SG CYS U 54 " distance=2.04 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 158 " distance=2.04 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 54 " distance=2.04 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: 38.52 Conformation dependent library (CDL) restraints added in 4.7 seconds 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 164 helices and 18 sheets defined 48.3% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.63 Creating SS restraints... Processing helix chain 'N' and resid 5 through 9 removed outlier: 3.595A pdb=" N GLN N 9 " --> pdb=" O ALA N 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 5 through 9' Processing helix chain 'N' and resid 55 through 62 removed outlier: 4.256A pdb=" N GLU N 60 " --> pdb=" O GLY N 56 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS N 61 " --> pdb=" O TYR N 57 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU N 62 " --> pdb=" O PHE N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 80 removed outlier: 3.858A pdb=" N VAL N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU N 80 " --> pdb=" O GLU N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 117 removed outlier: 4.011A pdb=" N GLU N 111 " --> pdb=" O PRO N 107 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU N 112 " --> pdb=" O LYS N 108 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA N 114 " --> pdb=" O VAL N 110 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP N 115 " --> pdb=" O GLU N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 141 removed outlier: 3.687A pdb=" N LYS N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU N 135 " --> pdb=" O ARG N 131 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN N 139 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 157 removed outlier: 3.526A pdb=" N PHE N 150 " --> pdb=" O ARG N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 164 No H-bonds generated for 'chain 'N' and resid 162 through 164' Processing helix chain 'N' and resid 171 through 175 Processing helix chain 'N' and resid 179 through 189 removed outlier: 3.606A pdb=" N ARG N 188 " --> pdb=" O GLU N 184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS N 189 " --> pdb=" O TYR N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 194 No H-bonds generated for 'chain 'N' and resid 192 through 194' Processing helix chain 'N' and resid 209 through 214 Processing helix chain 'N' and resid 216 through 218 No H-bonds generated for 'chain 'N' and resid 216 through 218' Processing helix chain 'N' and resid 265 through 277 removed outlier: 4.140A pdb=" N GLN N 271 " --> pdb=" O VAL N 268 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN N 274 " --> pdb=" O GLN N 271 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 289 No H-bonds generated for 'chain 'N' and resid 287 through 289' Processing helix chain 'N' and resid 293 through 300 removed outlier: 3.635A pdb=" N ALA N 298 " --> pdb=" O LEU N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 328 through 347 removed outlier: 3.975A pdb=" N ILE N 331 " --> pdb=" O HIS N 328 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP N 332 " --> pdb=" O MET N 329 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP N 333 " --> pdb=" O SER N 330 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET N 335 " --> pdb=" O ASP N 332 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN N 339 " --> pdb=" O PHE N 336 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET N 343 " --> pdb=" O GLY N 340 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS N 346 " --> pdb=" O MET N 343 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 369 removed outlier: 3.963A pdb=" N ARG N 356 " --> pdb=" O SER N 352 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY N 357 " --> pdb=" O GLU N 353 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN N 363 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER N 367 " --> pdb=" O ASN N 363 " (cutoff:3.500A) Processing helix chain 'N' and resid 373 through 385 removed outlier: 4.523A pdb=" N LEU N 384 " --> pdb=" O GLY N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 400 removed outlier: 3.601A pdb=" N SER N 397 " --> pdb=" O ALA N 393 " (cutoff:3.500A) Processing helix chain 'N' and resid 404 through 414 removed outlier: 3.555A pdb=" N ARG N 408 " --> pdb=" O ALA N 404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU N 409 " --> pdb=" O ARG N 405 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER N 412 " --> pdb=" O ARG N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 439 Processing helix chain 'O' and resid 55 through 57 No H-bonds generated for 'chain 'O' and resid 55 through 57' Processing helix chain 'O' and resid 65 through 71 Processing helix chain 'O' and resid 82 through 92 removed outlier: 3.722A pdb=" N THR O 86 " --> pdb=" O SER O 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU O 90 " --> pdb=" O THR O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 127 removed outlier: 3.986A pdb=" N VAL O 116 " --> pdb=" O ARG O 113 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASP O 117 " --> pdb=" O ASP O 114 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE O 118 " --> pdb=" O ASP O 115 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET O 120 " --> pdb=" O ASP O 117 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU O 124 " --> pdb=" O GLU O 121 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN O 125 " --> pdb=" O PHE O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 141 removed outlier: 3.697A pdb=" N ALA O 138 " --> pdb=" O ARG O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 153 removed outlier: 3.656A pdb=" N ALA O 149 " --> pdb=" O ARG O 145 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA O 151 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU O 152 " --> pdb=" O LYS O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 166 removed outlier: 3.680A pdb=" N HIS O 158 " --> pdb=" O PRO O 155 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE O 160 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU O 161 " --> pdb=" O HIS O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 198 removed outlier: 4.639A pdb=" N TYR O 194 " --> pdb=" O GLU O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 223 removed outlier: 3.643A pdb=" N GLU O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 279 removed outlier: 3.514A pdb=" N ALA O 271 " --> pdb=" O ALA O 267 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL O 274 " --> pdb=" O ASN O 270 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS O 277 " --> pdb=" O SER O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 299 Processing helix chain 'O' and resid 334 through 348 removed outlier: 4.560A pdb=" N ALA O 339 " --> pdb=" O ASP O 335 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN O 342 " --> pdb=" O LYS O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 354 through 371 removed outlier: 4.010A pdb=" N LEU O 369 " --> pdb=" O LYS O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 388 removed outlier: 3.677A pdb=" N GLU O 381 " --> pdb=" O GLY O 377 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY O 383 " --> pdb=" O LEU O 379 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER O 384 " --> pdb=" O ASP O 380 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN O 385 " --> pdb=" O GLU O 381 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA O 386 " --> pdb=" O VAL O 382 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA O 388 " --> pdb=" O SER O 384 " (cutoff:3.500A) Processing helix chain 'O' and resid 395 through 403 Processing helix chain 'O' and resid 410 through 419 removed outlier: 3.900A pdb=" N ALA O 414 " --> pdb=" O VAL O 410 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 16 Processing helix chain 'P' and resid 33 through 53 removed outlier: 3.927A pdb=" N LEU P 37 " --> pdb=" O PHE P 33 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY P 38 " --> pdb=" O GLY P 34 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE P 39 " --> pdb=" O SER P 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE P 50 " --> pdb=" O LEU P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 72 removed outlier: 4.265A pdb=" N PHE P 63 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER P 64 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 104 removed outlier: 3.872A pdb=" N PHE P 91 " --> pdb=" O ALA P 87 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET P 96 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY P 99 " --> pdb=" O TYR P 95 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY P 101 " --> pdb=" O HIS P 97 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU P 102 " --> pdb=" O VAL P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 132 removed outlier: 3.739A pdb=" N ASN P 114 " --> pdb=" O LEU P 110 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE P 115 " --> pdb=" O GLU P 111 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU P 120 " --> pdb=" O GLY P 116 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE P 128 " --> pdb=" O MET P 124 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET P 129 " --> pdb=" O ALA P 125 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL P 132 " --> pdb=" O PHE P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 152 removed outlier: 3.516A pdb=" N ILE P 146 " --> pdb=" O GLY P 142 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU P 149 " --> pdb=" O VAL P 145 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU P 150 " --> pdb=" O ILE P 146 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER P 151 " --> pdb=" O THR P 147 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA P 152 " --> pdb=" O ASN P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 164 Processing helix chain 'P' and resid 172 through 201 removed outlier: 3.666A pdb=" N PHE P 178 " --> pdb=" O THR P 174 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA P 180 " --> pdb=" O THR P 176 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE P 181 " --> pdb=" O ARG P 177 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE P 184 " --> pdb=" O ALA P 180 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU P 185 " --> pdb=" O PHE P 181 " (cutoff:3.500A) Proline residue: P 186 - end of helix removed outlier: 3.836A pdb=" N MET P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU P 200 " --> pdb=" O HIS P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 216 No H-bonds generated for 'chain 'P' and resid 214 through 216' Processing helix chain 'P' and resid 223 through 245 removed outlier: 4.783A pdb=" N LEU P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 256 Processing helix chain 'P' and resid 272 through 283 removed outlier: 4.257A pdb=" N PHE P 276 " --> pdb=" O TYR P 273 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR P 278 " --> pdb=" O LEU P 275 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA P 279 " --> pdb=" O PHE P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 288 through 303 removed outlier: 4.006A pdb=" N ALA P 293 " --> pdb=" O GLY P 289 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU P 301 " --> pdb=" O SER P 297 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA P 302 " --> pdb=" O ILE P 298 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU P 303 " --> pdb=" O LEU P 299 " (cutoff:3.500A) Processing helix chain 'P' and resid 305 through 307 No H-bonds generated for 'chain 'P' and resid 305 through 307' Processing helix chain 'P' and resid 319 through 338 removed outlier: 3.786A pdb=" N ALA P 327 " --> pdb=" O CYS P 323 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP P 337 " --> pdb=" O LEU P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 363 removed outlier: 3.560A pdb=" N THR P 349 " --> pdb=" O HIS P 345 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE P 350 " --> pdb=" O PRO P 346 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU P 353 " --> pdb=" O THR P 349 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL P 356 " --> pdb=" O GLN P 352 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE P 362 " --> pdb=" O TYR P 358 " (cutoff:3.500A) Processing helix chain 'P' and resid 365 through 373 removed outlier: 3.768A pdb=" N GLY P 370 " --> pdb=" O MET P 366 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 35 removed outlier: 3.506A pdb=" N GLY Q 29 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN Q 31 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 48 through 50 No H-bonds generated for 'chain 'Q' and resid 48 through 50' Processing helix chain 'Q' and resid 58 through 67 removed outlier: 3.691A pdb=" N LEU Q 64 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 103 Processing helix chain 'Q' and resid 124 through 133 Processing helix chain 'Q' and resid 179 through 193 removed outlier: 3.618A pdb=" N TRP Q 192 " --> pdb=" O THR Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 198 through 231 removed outlier: 3.677A pdb=" N ARG Q 203 " --> pdb=" O ASP Q 199 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU Q 209 " --> pdb=" O GLY Q 205 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU Q 210 " --> pdb=" O LEU Q 206 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU Q 214 " --> pdb=" O LEU Q 210 " (cutoff:3.500A) Proline residue: Q 217 - end of helix removed outlier: 4.962A pdb=" N VAL Q 229 " --> pdb=" O HIS Q 225 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 18 No H-bonds generated for 'chain 'R' and resid 16 through 18' Processing helix chain 'R' and resid 29 through 62 removed outlier: 3.572A pdb=" N SER R 36 " --> pdb=" O ARG R 32 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER R 56 " --> pdb=" O LYS R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 70 Processing helix chain 'R' and resid 109 through 111 No H-bonds generated for 'chain 'R' and resid 109 through 111' Processing helix chain 'R' and resid 123 through 126 No H-bonds generated for 'chain 'R' and resid 123 through 126' Processing helix chain 'S' and resid 17 through 23 removed outlier: 3.609A pdb=" N ASN S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 41 through 49 removed outlier: 3.946A pdb=" N ALA S 46 " --> pdb=" O ASP S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 71 removed outlier: 3.764A pdb=" N ASP S 57 " --> pdb=" O ASN S 53 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG S 61 " --> pdb=" O ASP S 57 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP S 67 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG S 71 " --> pdb=" O ASP S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 85 No H-bonds generated for 'chain 'S' and resid 83 through 85' Processing helix chain 'S' and resid 91 through 106 removed outlier: 3.791A pdb=" N VAL S 97 " --> pdb=" O TYR S 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 42 Proline residue: T 35 - end of helix Processing helix chain 'T' and resid 45 through 70 removed outlier: 4.558A pdb=" N ALA T 49 " --> pdb=" O LEU T 46 " (cutoff:3.500A) Proline residue: T 50 - end of helix removed outlier: 3.871A pdb=" N TYR T 59 " --> pdb=" O TYR T 56 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TRP T 61 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY T 62 " --> pdb=" O TYR T 59 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN T 64 " --> pdb=" O TRP T 61 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU T 65 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS T 68 " --> pdb=" O GLU T 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 24 removed outlier: 3.624A pdb=" N VAL U 20 " --> pdb=" O PRO U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 45 Processing helix chain 'U' and resid 55 through 70 removed outlier: 3.864A pdb=" N LEU U 59 " --> pdb=" O THR U 55 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP U 60 " --> pdb=" O GLU U 56 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS U 67 " --> pdb=" O HIS U 63 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS U 68 " --> pdb=" O ALA U 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 75 No H-bonds generated for 'chain 'U' and resid 73 through 75' Processing helix chain 'W' and resid 5 through 12 removed outlier: 3.730A pdb=" N LEU W 12 " --> pdb=" O ARG W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 46 removed outlier: 3.764A pdb=" N ILE W 24 " --> pdb=" O PHE W 20 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL W 26 " --> pdb=" O LEU W 22 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG W 33 " --> pdb=" O LEU W 29 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN W 37 " --> pdb=" O ARG W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 55 No H-bonds generated for 'chain 'W' and resid 53 through 55' Processing helix chain 'A' and resid 5 through 9 removed outlier: 3.596A pdb=" N GLN A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 9' Processing helix chain 'A' and resid 55 through 62 removed outlier: 4.258A pdb=" N GLU A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS A 61 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 62 " --> pdb=" O PHE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.858A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 4.010A pdb=" N GLU A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 removed outlier: 3.686A pdb=" N LYS A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.526A pdb=" N PHE A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.605A pdb=" N ARG A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 265 through 277 removed outlier: 4.139A pdb=" N GLN A 271 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 274 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.634A pdb=" N ALA A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 347 removed outlier: 3.976A pdb=" N ILE A 331 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP A 332 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 335 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 339 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET A 343 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 346 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.963A pdb=" N ARG A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN A 363 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 4.522A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 400 removed outlier: 3.601A pdb=" N SER A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.554A pdb=" N ARG A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 65 through 71 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.721A pdb=" N THR B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.988A pdb=" N VAL B 116 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASP B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 118 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET B 120 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 124 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.697A pdb=" N ALA B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.654A pdb=" N ALA B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.681A pdb=" N HIS B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 161 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 198 removed outlier: 4.639A pdb=" N TYR B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 removed outlier: 3.643A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 removed outlier: 3.514A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 Processing helix chain 'B' and resid 334 through 348 removed outlier: 4.561A pdb=" N ALA B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 371 removed outlier: 4.008A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 388 removed outlier: 3.678A pdb=" N GLU B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 410 through 419 removed outlier: 3.901A pdb=" N ALA B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 33 through 53 removed outlier: 3.926A pdb=" N LEU C 37 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 72 removed outlier: 4.265A pdb=" N PHE C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 104 removed outlier: 3.872A pdb=" N PHE C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET C 96 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY C 101 " --> pdb=" O HIS C 97 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 132 removed outlier: 3.740A pdb=" N ASN C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C 128 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 152 removed outlier: 3.516A pdb=" N ILE C 146 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 149 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA C 152 " --> pdb=" O ASN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 164 Processing helix chain 'C' and resid 172 through 201 removed outlier: 3.665A pdb=" N PHE C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) Proline residue: C 186 - end of helix removed outlier: 3.836A pdb=" N MET C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'C' and resid 223 through 245 removed outlier: 4.783A pdb=" N LEU C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 272 through 283 removed outlier: 4.257A pdb=" N PHE C 276 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 278 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA C 279 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 303 removed outlier: 4.008A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 319 through 338 removed outlier: 3.785A pdb=" N ALA C 327 " --> pdb=" O CYS C 323 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 363 removed outlier: 3.560A pdb=" N THR C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 350 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 362 " --> pdb=" O TYR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 373 removed outlier: 3.768A pdb=" N GLY C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 removed outlier: 3.506A pdb=" N GLY D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 58 through 67 removed outlier: 3.691A pdb=" N LEU D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 179 through 193 removed outlier: 3.617A pdb=" N TRP D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 231 removed outlier: 3.676A pdb=" N ARG D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU D 209 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Proline residue: D 217 - end of helix removed outlier: 4.961A pdb=" N VAL D 229 " --> pdb=" O HIS D 225 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 29 through 62 removed outlier: 3.573A pdb=" N SER E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 109 through 111 No H-bonds generated for 'chain 'E' and resid 109 through 111' Processing helix chain 'E' and resid 123 through 126 No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'F' and resid 17 through 23 removed outlier: 3.608A pdb=" N ASN F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 36 No H-bonds generated for 'chain 'F' and resid 34 through 36' Processing helix chain 'F' and resid 41 through 49 removed outlier: 3.945A pdb=" N ALA F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.764A pdb=" N ASP F 57 " --> pdb=" O ASN F 53 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 71 " --> pdb=" O ASP F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 91 through 106 removed outlier: 3.790A pdb=" N VAL F 97 " --> pdb=" O TYR F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 42 Proline residue: G 35 - end of helix Processing helix chain 'G' and resid 45 through 70 removed outlier: 4.558A pdb=" N ALA G 49 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Proline residue: G 50 - end of helix removed outlier: 3.870A pdb=" N TYR G 59 " --> pdb=" O TYR G 56 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TRP G 61 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY G 62 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN G 64 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU G 65 " --> pdb=" O GLY G 62 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS G 68 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 24 removed outlier: 3.624A pdb=" N VAL H 20 " --> pdb=" O PRO H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 45 Processing helix chain 'H' and resid 55 through 70 removed outlier: 3.863A pdb=" N LEU H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS H 67 " --> pdb=" O HIS H 63 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'J' and resid 5 through 12 removed outlier: 3.731A pdb=" N LEU J 12 " --> pdb=" O ARG J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 46 removed outlier: 3.766A pdb=" N ILE J 24 " --> pdb=" O PHE J 20 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN J 37 " --> pdb=" O ARG J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' Processing sheet with id= A, first strand: chain 'N' and resid 15 through 17 Processing sheet with id= B, first strand: chain 'N' and resid 198 through 201 removed outlier: 3.585A pdb=" N TYR N 97 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 421 through 425 removed outlier: 3.778A pdb=" N ALA N 251 " --> pdb=" O CYS N 326 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS N 326 " --> pdb=" O ALA N 251 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'O' and resid 25 through 28 removed outlier: 3.840A pdb=" N SER O 37 " --> pdb=" O GLU O 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR O 27 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE O 35 " --> pdb=" O THR O 27 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'O' and resid 95 through 97 removed outlier: 3.988A pdb=" N GLU O 110 " --> pdb=" O LYS O 95 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'O' and resid 243 through 247 removed outlier: 8.500A pdb=" N ILE O 244 " --> pdb=" O LYS O 422 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET O 424 " --> pdb=" O ILE O 244 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLU O 246 " --> pdb=" O MET O 424 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA O 426 " --> pdb=" O GLU O 246 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA O 255 " --> pdb=" O THR O 326 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'Q' and resid 69 through 71 Processing sheet with id= H, first strand: chain 'R' and resid 87 through 91 Processing sheet with id= I, first strand: chain 'V' and resid 65 through 67 removed outlier: 3.594A pdb=" N SER V 67 " --> pdb=" O SER V 75 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 15 through 17 Processing sheet with id= K, first strand: chain 'A' and resid 198 through 201 removed outlier: 3.586A pdb=" N TYR A 97 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 421 through 425 removed outlier: 3.778A pdb=" N ALA A 251 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS A 326 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.842A pdb=" N SER B 37 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 27 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 35 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.988A pdb=" N GLU B 110 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 243 through 247 removed outlier: 8.500A pdb=" N ILE B 244 " --> pdb=" O LYS B 422 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET B 424 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLU B 246 " --> pdb=" O MET B 424 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B 426 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 255 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 69 through 71 Processing sheet with id= Q, first strand: chain 'E' and resid 87 through 91 Processing sheet with id= R, first strand: chain 'I' and resid 65 through 67 removed outlier: 3.593A pdb=" N SER I 67 " --> pdb=" O SER I 75 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 2886 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: 20.68 Time building geometry restraints manager: 40.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.10: 30310 1.10 - 1.38: 12437 1.38 - 1.65: 19121 1.65 - 1.92: 242 1.92 - 2.20: 22 Bond restraints: 62132 Sorted by residual: bond pdb=" N ARG I 62 " pdb=" H1 ARG I 62 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" N ARG V 62 " pdb=" H1 ARG V 62 " ideal model delta sigma weight residual 0.960 0.863 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C18 G8U C 503 " pdb=" O23 G8U C 503 " ideal model delta sigma weight residual 1.328 1.397 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C VAL O 186 " pdb=" N THR O 187 " ideal model delta sigma weight residual 1.333 1.238 0.094 2.74e-02 1.33e+03 1.19e+01 bond pdb=" C18 G8U P 503 " pdb=" O23 G8U P 503 " ideal model delta sigma weight residual 1.328 1.397 -0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 62127 not shown) Histogram of bond angle deviations from ideal: 71.00 - 90.38: 53 90.38 - 109.76: 45833 109.76 - 129.15: 65814 129.15 - 148.53: 392 148.53 - 167.92: 12 Bond angle restraints: 112104 Sorted by residual: angle pdb=" N ALA E 176 " pdb=" CA ALA E 176 " pdb=" HA ALA E 176 " ideal model delta sigma weight residual 110.00 71.01 38.99 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C VAL O 186 " pdb=" CA VAL O 186 " pdb=" HA VAL O 186 " ideal model delta sigma weight residual 109.00 71.00 38.00 3.00e+00 1.11e-01 1.60e+02 angle pdb=" N VAL O 186 " pdb=" CA VAL O 186 " pdb=" HA VAL O 186 " ideal model delta sigma weight residual 110.00 72.53 37.47 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C ALA E 176 " pdb=" CA ALA E 176 " pdb=" HA ALA E 176 " ideal model delta sigma weight residual 109.00 72.91 36.09 3.00e+00 1.11e-01 1.45e+02 angle pdb=" CB ALA E 176 " pdb=" CA ALA E 176 " pdb=" HA ALA E 176 " ideal model delta sigma weight residual 109.00 74.58 34.42 3.00e+00 1.11e-01 1.32e+02 ... (remaining 112099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 27648 17.69 - 35.38: 1175 35.38 - 53.06: 348 53.06 - 70.75: 121 70.75 - 88.44: 18 Dihedral angle restraints: 29310 sinusoidal: 15760 harmonic: 13550 Sorted by residual: dihedral pdb=" CA GLY E 174 " pdb=" C GLY E 174 " pdb=" N PRO E 175 " pdb=" CA PRO E 175 " ideal model delta harmonic sigma weight residual 180.00 135.97 44.03 0 5.00e+00 4.00e-02 7.76e+01 dihedral pdb=" CA GLY R 174 " pdb=" C GLY R 174 " pdb=" N PRO R 175 " pdb=" CA PRO R 175 " ideal model delta harmonic sigma weight residual 180.00 136.01 43.99 0 5.00e+00 4.00e-02 7.74e+01 dihedral pdb=" CA ASN P 15 " pdb=" C ASN P 15 " pdb=" N ASN P 16 " pdb=" CA ASN P 16 " ideal model delta harmonic sigma weight residual 180.00 148.03 31.97 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 29307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4639 0.117 - 0.235: 109 0.235 - 0.352: 0 0.352 - 0.469: 0 0.469 - 0.587: 2 Chirality restraints: 4750 Sorted by residual: chirality pdb=" CB VAL I 64 " pdb=" CA VAL I 64 " pdb=" CG1 VAL I 64 " pdb=" CG2 VAL I 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" CB VAL V 64 " pdb=" CA VAL V 64 " pdb=" CG1 VAL V 64 " pdb=" CG2 VAL V 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" CB VAL N 39 " pdb=" CA VAL N 39 " pdb=" CG1 VAL N 39 " pdb=" CG2 VAL N 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 4747 not shown) Planarity restraints: 9200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN P 44 " 0.242 2.00e-02 2.50e+03 2.91e-01 1.27e+03 pdb=" CD GLN P 44 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN P 44 " -0.226 2.00e-02 2.50e+03 pdb=" NE2 GLN P 44 " 0.014 2.00e-02 2.50e+03 pdb="HE21 GLN P 44 " -0.439 2.00e-02 2.50e+03 pdb="HE22 GLN P 44 " 0.452 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 44 " -0.240 2.00e-02 2.50e+03 2.86e-01 1.23e+03 pdb=" CD GLN C 44 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN C 44 " 0.224 2.00e-02 2.50e+03 pdb=" NE2 GLN C 44 " -0.014 2.00e-02 2.50e+03 pdb="HE21 GLN C 44 " 0.431 2.00e-02 2.50e+03 pdb="HE22 GLN C 44 " -0.442 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN N 435 " 0.124 2.00e-02 2.50e+03 1.35e-01 2.74e+02 pdb=" CG ASN N 435 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN N 435 " -0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN N 435 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN N 435 " -0.200 2.00e-02 2.50e+03 pdb="HD22 ASN N 435 " 0.201 2.00e-02 2.50e+03 ... (remaining 9197 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 4969 2.22 - 2.81: 138235 2.81 - 3.41: 155517 3.41 - 4.00: 212959 4.00 - 4.60: 336851 Nonbonded interactions: 848531 Sorted by model distance: nonbonded pdb=" O LEU O 163 " pdb=" H ALA O 167 " model vdw 1.622 1.850 nonbonded pdb=" O LEU B 163 " pdb=" H ALA B 167 " model vdw 1.622 1.850 nonbonded pdb=" O ILE C 164 " pdb="HH21 ARG C 177 " model vdw 1.636 1.850 nonbonded pdb=" O ILE P 164 " pdb="HH21 ARG P 177 " model vdw 1.638 1.850 nonbonded pdb=" O VAL C 215 " pdb=" HZ3 LYS F 63 " model vdw 1.640 1.850 ... (remaining 848526 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 'A' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'G' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 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: 0.660 Extract box with map and model: 4.290 Check model and map are aligned: 0.650 Set scattering table: 0.430 Process input model: 152.060 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.440 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.012 0.171 31772 Z= 0.766 Angle : 0.962 23.879 43226 Z= 0.478 Chirality : 0.052 0.587 4750 Planarity : 0.006 0.074 5514 Dihedral : 9.174 88.440 11462 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.18 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.11), residues: 3850 helix: -3.17 (0.08), residues: 1866 sheet: -3.32 (0.26), residues: 276 loop : -2.64 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP P 141 HIS 0.017 0.003 HIS B 158 PHE 0.029 0.003 PHE S 26 TYR 0.025 0.003 TYR N 47 ARG 0.011 0.001 ARG P 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 946 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 946 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 294 LEU cc_start: 0.8949 (tp) cc_final: 0.8624 (tp) REVERT: P 70 CYS cc_start: 0.8373 (m) cc_final: 0.8076 (t) REVERT: P 96 MET cc_start: 0.7855 (mmt) cc_final: 0.7555 (mmm) REVERT: P 190 MET cc_start: 0.7731 (ttp) cc_final: 0.7514 (ttp) REVERT: P 287 LYS cc_start: 0.8592 (tttt) cc_final: 0.8384 (tptm) REVERT: P 311 LYS cc_start: 0.8874 (mttm) cc_final: 0.8465 (mtpp) REVERT: P 349 THR cc_start: 0.8627 (m) cc_final: 0.8398 (t) REVERT: Q 44 ASP cc_start: 0.7772 (m-30) cc_final: 0.7567 (t0) REVERT: Q 66 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6815 (mm-30) REVERT: Q 77 ASP cc_start: 0.8095 (m-30) cc_final: 0.7383 (t0) REVERT: Q 166 ASN cc_start: 0.8295 (t0) cc_final: 0.7939 (t0) REVERT: R 23 LYS cc_start: 0.7566 (mmtm) cc_final: 0.7165 (mmtt) REVERT: R 186 GLU cc_start: 0.7783 (tt0) cc_final: 0.7421 (tm-30) REVERT: S 44 LYS cc_start: 0.9035 (mttt) cc_final: 0.8700 (mtmt) REVERT: S 60 PHE cc_start: 0.8391 (t80) cc_final: 0.8158 (t80) REVERT: S 109 LYS cc_start: 0.8560 (mttt) cc_final: 0.8295 (mttt) REVERT: T 24 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7070 (tpt170) REVERT: B 63 LEU cc_start: 0.8547 (mt) cc_final: 0.8233 (tp) REVERT: B 132 PHE cc_start: 0.8491 (m-10) cc_final: 0.8269 (m-10) REVERT: B 243 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6508 (tm-30) REVERT: C 70 CYS cc_start: 0.8356 (m) cc_final: 0.8150 (t) REVERT: C 96 MET cc_start: 0.7866 (mmt) cc_final: 0.7430 (mmm) REVERT: C 155 TYR cc_start: 0.6272 (m-10) cc_final: 0.6062 (t80) REVERT: C 172 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8319 (tttp) REVERT: C 311 LYS cc_start: 0.8802 (mttm) cc_final: 0.8367 (mtpp) REVERT: D 22 ASP cc_start: 0.7132 (t0) cc_final: 0.6700 (t0) REVERT: D 66 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6715 (mm-30) REVERT: D 77 ASP cc_start: 0.8259 (m-30) cc_final: 0.7298 (t0) REVERT: D 153 PHE cc_start: 0.8101 (t80) cc_final: 0.7777 (t80) REVERT: D 228 SER cc_start: 0.9148 (p) cc_final: 0.8741 (t) REVERT: E 23 LYS cc_start: 0.7639 (mmtm) cc_final: 0.7387 (mmtt) REVERT: E 131 GLU cc_start: 0.6813 (pm20) cc_final: 0.6520 (tp30) REVERT: E 186 GLU cc_start: 0.7920 (tt0) cc_final: 0.7403 (tm-30) REVERT: F 14 GLU cc_start: 0.8049 (tp30) cc_final: 0.7713 (tm-30) REVERT: F 109 LYS cc_start: 0.8370 (mttt) cc_final: 0.8084 (mttt) REVERT: G 24 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7052 (tpt170) REVERT: J 16 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6911 (tpt170) outliers start: 0 outliers final: 0 residues processed: 946 average time/residue: 0.9834 time to fit residues: 1377.0899 Evaluate side-chains 471 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 0.3980 chunk 288 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 297 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 chunk 345 optimal weight: 20.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 118 GLN N 252 HIS ** N 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 ASN O 343 GLN Q 31 GLN Q 75 ASN R 53 ASN A 252 HIS B 343 GLN D 31 GLN E 53 ASN H 26 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 31772 Z= 0.201 Angle : 0.635 11.873 43226 Z= 0.321 Chirality : 0.045 1.432 4750 Planarity : 0.005 0.063 5514 Dihedral : 7.812 89.767 4322 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -3.03 (0.13), residues: 3850 helix: -1.81 (0.10), residues: 1924 sheet: -2.46 (0.27), residues: 314 loop : -1.98 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 379 HIS 0.006 0.001 HIS P 68 PHE 0.013 0.001 PHE P 274 TYR 0.019 0.001 TYR Q 220 ARG 0.006 0.000 ARG U 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 672 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 45 SER cc_start: 0.8833 (p) cc_final: 0.8419 (t) REVERT: N 297 ILE cc_start: 0.8712 (mt) cc_final: 0.8436 (mm) REVERT: O 146 ILE cc_start: 0.7992 (mt) cc_final: 0.7553 (tp) REVERT: P 10 LEU cc_start: 0.5683 (tp) cc_final: 0.5084 (tt) REVERT: P 96 MET cc_start: 0.7550 (mmt) cc_final: 0.7052 (mmm) REVERT: P 228 ASP cc_start: 0.8369 (m-30) cc_final: 0.8162 (m-30) REVERT: P 287 LYS cc_start: 0.8558 (tttt) cc_final: 0.8318 (tptm) REVERT: Q 66 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7165 (mm-30) REVERT: Q 150 ASN cc_start: 0.8356 (t0) cc_final: 0.8006 (t0) REVERT: Q 153 PHE cc_start: 0.8208 (t80) cc_final: 0.7863 (t80) REVERT: Q 166 ASN cc_start: 0.8305 (t0) cc_final: 0.7959 (t0) REVERT: Q 222 MET cc_start: 0.8848 (mtp) cc_final: 0.7961 (mmm) REVERT: R 12 ASP cc_start: 0.6380 (t0) cc_final: 0.6068 (t0) REVERT: R 23 LYS cc_start: 0.7496 (mmtm) cc_final: 0.7170 (mmtt) REVERT: R 186 GLU cc_start: 0.7901 (tt0) cc_final: 0.7507 (tm-30) REVERT: S 60 PHE cc_start: 0.8422 (t80) cc_final: 0.8111 (t80) REVERT: S 109 LYS cc_start: 0.8428 (mttt) cc_final: 0.8209 (mttt) REVERT: T 24 ARG cc_start: 0.7814 (ttm110) cc_final: 0.6989 (tpt170) REVERT: V 70 LEU cc_start: 0.8543 (tp) cc_final: 0.8234 (tp) REVERT: W 33 ARG cc_start: 0.6745 (ttm170) cc_final: 0.6199 (mmp-170) REVERT: B 63 LEU cc_start: 0.8691 (mt) cc_final: 0.8312 (tp) REVERT: B 146 ILE cc_start: 0.8351 (mm) cc_final: 0.7904 (tp) REVERT: B 243 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6451 (tm-30) REVERT: B 261 SER cc_start: 0.7750 (t) cc_final: 0.7453 (p) REVERT: C 53 MET cc_start: 0.8295 (mtm) cc_final: 0.7517 (mtt) REVERT: C 96 MET cc_start: 0.7615 (mmt) cc_final: 0.7221 (mmm) REVERT: C 138 MET cc_start: 0.7322 (mmm) cc_final: 0.6952 (mtt) REVERT: C 172 LYS cc_start: 0.8590 (ttpt) cc_final: 0.7923 (tttp) REVERT: C 311 LYS cc_start: 0.8742 (mttm) cc_final: 0.8377 (mtpp) REVERT: D 66 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7081 (mm-30) REVERT: D 153 PHE cc_start: 0.7990 (t80) cc_final: 0.7667 (t80) REVERT: D 222 MET cc_start: 0.8978 (mtp) cc_final: 0.8238 (mmm) REVERT: D 228 SER cc_start: 0.8910 (p) cc_final: 0.8592 (t) REVERT: E 23 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7369 (mmtt) REVERT: E 40 THR cc_start: 0.9217 (m) cc_final: 0.9015 (m) REVERT: E 131 GLU cc_start: 0.6897 (pm20) cc_final: 0.6396 (tp30) REVERT: E 186 GLU cc_start: 0.7905 (tt0) cc_final: 0.7391 (tm-30) REVERT: G 24 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7014 (tpt170) REVERT: H 24 CYS cc_start: 0.5299 (t) cc_final: 0.4822 (t) REVERT: J 16 ARG cc_start: 0.7247 (ttm-80) cc_final: 0.6949 (tpt170) REVERT: J 18 SER cc_start: 0.8347 (p) cc_final: 0.7981 (p) outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.8223 time to fit residues: 875.5685 Evaluate side-chains 456 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 345 optimal weight: 30.0000 chunk 373 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 94 HIS R 57 GLN A 173 ASN E 57 GLN G 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 31772 Z= 0.388 Angle : 0.689 14.835 43226 Z= 0.345 Chirality : 0.046 1.443 4750 Planarity : 0.005 0.065 5514 Dihedral : 7.442 89.933 4322 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.03 % Allowed : 1.25 % Favored : 98.72 % 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: -2.73 (0.13), residues: 3850 helix: -1.26 (0.11), residues: 1934 sheet: -2.55 (0.27), residues: 320 loop : -2.23 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 379 HIS 0.010 0.002 HIS O 198 PHE 0.024 0.002 PHE E 187 TYR 0.015 0.002 TYR P 224 ARG 0.006 0.001 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 608 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 607 time to evaluate : 3.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: N 45 SER cc_start: 0.8941 (p) cc_final: 0.8563 (t) REVERT: N 294 LEU cc_start: 0.9320 (tp) cc_final: 0.9016 (tp) REVERT: O 223 PHE cc_start: 0.6558 (m-80) cc_final: 0.6136 (m-80) REVERT: P 44 GLN cc_start: 0.8469 (tt0) cc_final: 0.7627 (mm110) REVERT: P 96 MET cc_start: 0.8183 (mmt) cc_final: 0.7791 (mmm) REVERT: P 155 TYR cc_start: 0.6446 (m-10) cc_final: 0.6185 (t80) REVERT: P 228 ASP cc_start: 0.8498 (m-30) cc_final: 0.8283 (m-30) REVERT: P 287 LYS cc_start: 0.8563 (tttt) cc_final: 0.8337 (tptm) REVERT: P 311 LYS cc_start: 0.9069 (mttm) cc_final: 0.8805 (mtpp) REVERT: Q 66 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7380 (tp30) REVERT: Q 153 PHE cc_start: 0.8281 (t80) cc_final: 0.8013 (t80) REVERT: Q 166 ASN cc_start: 0.8418 (t0) cc_final: 0.7886 (t0) REVERT: Q 222 MET cc_start: 0.9043 (mtp) cc_final: 0.8458 (mmm) REVERT: Q 228 SER cc_start: 0.9024 (p) cc_final: 0.8702 (t) REVERT: R 23 LYS cc_start: 0.7874 (mmtm) cc_final: 0.7494 (mmtt) REVERT: T 24 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7075 (tpt170) REVERT: T 59 TYR cc_start: 0.8739 (t80) cc_final: 0.8479 (t80) REVERT: V 70 LEU cc_start: 0.8975 (tp) cc_final: 0.8711 (tp) REVERT: W 18 SER cc_start: 0.8144 (p) cc_final: 0.7651 (t) REVERT: W 33 ARG cc_start: 0.7070 (ttm170) cc_final: 0.6400 (mmp-170) REVERT: A 386 TYR cc_start: 0.5742 (m-80) cc_final: 0.5498 (m-80) REVERT: B 63 LEU cc_start: 0.8898 (mt) cc_final: 0.8583 (tp) REVERT: B 146 ILE cc_start: 0.8637 (mm) cc_final: 0.8169 (tp) REVERT: B 223 PHE cc_start: 0.6427 (m-80) cc_final: 0.5996 (m-80) REVERT: B 243 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6555 (tm-30) REVERT: C 96 MET cc_start: 0.8100 (mmt) cc_final: 0.7689 (mmm) REVERT: C 137 GLN cc_start: 0.7238 (tm-30) cc_final: 0.6963 (tp-100) REVERT: C 172 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8213 (tttp) REVERT: C 311 LYS cc_start: 0.9112 (mttm) cc_final: 0.8812 (mtpp) REVERT: C 323 CYS cc_start: 0.8347 (m) cc_final: 0.7848 (t) REVERT: D 66 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7117 (tp30) REVERT: D 228 SER cc_start: 0.9022 (p) cc_final: 0.8794 (t) REVERT: E 23 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7595 (mmtt) REVERT: E 131 GLU cc_start: 0.7167 (pm20) cc_final: 0.6440 (tp30) REVERT: G 24 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7145 (tpt170) REVERT: G 59 TYR cc_start: 0.8796 (t80) cc_final: 0.8520 (t80) REVERT: H 24 CYS cc_start: 0.5232 (t) cc_final: 0.4770 (t) REVERT: J 16 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7058 (tpt170) REVERT: J 18 SER cc_start: 0.8382 (p) cc_final: 0.8107 (p) outliers start: 1 outliers final: 1 residues processed: 608 average time/residue: 0.7900 time to fit residues: 760.9919 Evaluate side-chains 432 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 431 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 232 optimal weight: 0.6980 chunk 346 optimal weight: 8.9990 chunk 367 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 173 ASN Q 75 ASN Q 200 HIS U 26 GLN A 173 ASN G 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 31772 Z= 0.297 Angle : 0.594 11.415 43226 Z= 0.302 Chirality : 0.045 1.446 4750 Planarity : 0.005 0.118 5514 Dihedral : 7.064 89.351 4322 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -2.31 (0.13), residues: 3850 helix: -0.88 (0.11), residues: 1926 sheet: -2.15 (0.28), residues: 296 loop : -2.14 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 165 HIS 0.006 0.001 HIS Q 198 PHE 0.020 0.002 PHE P 274 TYR 0.013 0.001 TYR O 341 ARG 0.012 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 567 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 567 time to evaluate : 3.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 223 PHE cc_start: 0.6534 (m-80) cc_final: 0.6242 (m-80) REVERT: P 10 LEU cc_start: 0.5764 (tp) cc_final: 0.5208 (tt) REVERT: P 96 MET cc_start: 0.8174 (mmt) cc_final: 0.7808 (mmm) REVERT: P 155 TYR cc_start: 0.6450 (m-10) cc_final: 0.6249 (t80) REVERT: P 216 ASP cc_start: 0.8880 (t0) cc_final: 0.8671 (t0) REVERT: P 228 ASP cc_start: 0.8542 (m-30) cc_final: 0.8255 (m-30) REVERT: P 311 LYS cc_start: 0.9142 (mttm) cc_final: 0.8883 (mtpp) REVERT: P 323 CYS cc_start: 0.8319 (m) cc_final: 0.7794 (t) REVERT: Q 66 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7493 (tp30) REVERT: Q 153 PHE cc_start: 0.8232 (t80) cc_final: 0.7971 (t80) REVERT: Q 166 ASN cc_start: 0.8279 (t0) cc_final: 0.7950 (t0) REVERT: Q 228 SER cc_start: 0.9046 (p) cc_final: 0.8838 (t) REVERT: R 23 LYS cc_start: 0.7891 (mmtm) cc_final: 0.7611 (mmtt) REVERT: S 41 ASP cc_start: 0.8600 (p0) cc_final: 0.8080 (p0) REVERT: S 68 LEU cc_start: 0.8907 (mt) cc_final: 0.8695 (mt) REVERT: T 24 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7058 (tpt170) REVERT: T 59 TYR cc_start: 0.8771 (t80) cc_final: 0.8461 (t80) REVERT: U 27 LEU cc_start: 0.7857 (tp) cc_final: 0.7546 (mt) REVERT: V 70 LEU cc_start: 0.8973 (tp) cc_final: 0.8670 (tp) REVERT: W 18 SER cc_start: 0.8071 (p) cc_final: 0.7547 (t) REVERT: B 55 SER cc_start: 0.8408 (p) cc_final: 0.8161 (t) REVERT: B 63 LEU cc_start: 0.9029 (mt) cc_final: 0.8655 (tp) REVERT: B 146 ILE cc_start: 0.8629 (mm) cc_final: 0.8174 (tp) REVERT: B 223 PHE cc_start: 0.6664 (m-80) cc_final: 0.6219 (m-80) REVERT: B 243 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6534 (tm-30) REVERT: B 261 SER cc_start: 0.7981 (t) cc_final: 0.7661 (p) REVERT: C 96 MET cc_start: 0.8098 (mmt) cc_final: 0.7698 (mmm) REVERT: C 137 GLN cc_start: 0.7093 (tm-30) cc_final: 0.6792 (tm-30) REVERT: C 311 LYS cc_start: 0.9097 (mttm) cc_final: 0.8701 (mtpp) REVERT: C 323 CYS cc_start: 0.8398 (m) cc_final: 0.8023 (t) REVERT: D 222 MET cc_start: 0.8816 (mtp) cc_final: 0.8466 (mmm) REVERT: E 131 GLU cc_start: 0.7206 (pm20) cc_final: 0.6277 (tp30) REVERT: G 24 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7046 (tpt170) REVERT: G 59 TYR cc_start: 0.8785 (t80) cc_final: 0.8515 (t80) REVERT: J 16 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7121 (tpt170) REVERT: J 18 SER cc_start: 0.8316 (p) cc_final: 0.8053 (p) outliers start: 0 outliers final: 0 residues processed: 567 average time/residue: 0.8240 time to fit residues: 746.0045 Evaluate side-chains 415 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 215 HIS ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 ASN Q 200 HIS R 53 ASN R 57 GLN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 HIS ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 31772 Z= 0.424 Angle : 0.692 11.369 43226 Z= 0.351 Chirality : 0.047 1.426 4750 Planarity : 0.005 0.059 5514 Dihedral : 7.149 89.759 4322 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: -2.50 (0.13), residues: 3850 helix: -0.97 (0.11), residues: 1920 sheet: -2.29 (0.28), residues: 310 loop : -2.30 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP P 379 HIS 0.012 0.002 HIS D 198 PHE 0.017 0.002 PHE U 74 TYR 0.019 0.002 TYR O 341 ARG 0.007 0.001 ARG S 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 521 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 3.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 96 MET cc_start: 0.8339 (mmt) cc_final: 0.7980 (mmm) REVERT: P 311 LYS cc_start: 0.9181 (mttm) cc_final: 0.8921 (mtpp) REVERT: Q 153 PHE cc_start: 0.8314 (t80) cc_final: 0.8013 (t80) REVERT: Q 166 ASN cc_start: 0.8378 (t0) cc_final: 0.8001 (t0) REVERT: Q 222 MET cc_start: 0.8601 (mtp) cc_final: 0.8115 (tpp) REVERT: R 23 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7705 (mmtt) REVERT: T 59 TYR cc_start: 0.8875 (t80) cc_final: 0.8526 (t80) REVERT: U 27 LEU cc_start: 0.7808 (tp) cc_final: 0.7419 (mt) REVERT: V 70 LEU cc_start: 0.9156 (tp) cc_final: 0.8806 (tp) REVERT: W 18 SER cc_start: 0.8099 (p) cc_final: 0.7644 (t) REVERT: W 25 VAL cc_start: 0.8773 (t) cc_final: 0.8540 (p) REVERT: B 63 LEU cc_start: 0.9131 (mt) cc_final: 0.8869 (tp) REVERT: B 223 PHE cc_start: 0.6827 (m-80) cc_final: 0.6557 (m-80) REVERT: C 53 MET cc_start: 0.8492 (mtt) cc_final: 0.8256 (mtp) REVERT: C 75 TYR cc_start: 0.8071 (m-10) cc_final: 0.7834 (m-10) REVERT: C 96 MET cc_start: 0.8293 (mmt) cc_final: 0.7879 (mmm) REVERT: C 171 ASP cc_start: 0.9045 (t70) cc_final: 0.8791 (t70) REVERT: C 311 LYS cc_start: 0.9251 (mttm) cc_final: 0.8959 (mtpp) REVERT: C 323 CYS cc_start: 0.8431 (m) cc_final: 0.8016 (t) REVERT: E 53 ASN cc_start: 0.8518 (m-40) cc_final: 0.7593 (t0) REVERT: E 131 GLU cc_start: 0.7180 (pm20) cc_final: 0.5887 (tp30) REVERT: F 34 ASP cc_start: 0.7707 (m-30) cc_final: 0.7390 (m-30) REVERT: F 88 SER cc_start: 0.8122 (p) cc_final: 0.7896 (p) REVERT: J 16 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7320 (tpt170) REVERT: J 18 SER cc_start: 0.8403 (p) cc_final: 0.8127 (p) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.8141 time to fit residues: 679.4459 Evaluate side-chains 398 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 193 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 ASN Q 75 ASN A 126 GLN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 31772 Z= 0.262 Angle : 0.569 11.458 43226 Z= 0.289 Chirality : 0.045 1.466 4750 Planarity : 0.004 0.059 5514 Dihedral : 6.902 89.518 4322 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -2.02 (0.13), residues: 3850 helix: -0.59 (0.11), residues: 1916 sheet: -2.15 (0.29), residues: 288 loop : -2.03 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 379 HIS 0.005 0.001 HIS C 182 PHE 0.019 0.001 PHE C 274 TYR 0.023 0.001 TYR J 59 ARG 0.006 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 531 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 96 MET cc_start: 0.8349 (mmt) cc_final: 0.8009 (mmm) REVERT: P 139 SER cc_start: 0.9150 (m) cc_final: 0.8926 (m) REVERT: P 311 LYS cc_start: 0.9194 (mttm) cc_final: 0.8916 (mtpp) REVERT: P 323 CYS cc_start: 0.8396 (m) cc_final: 0.7994 (t) REVERT: Q 153 PHE cc_start: 0.8290 (t80) cc_final: 0.7961 (t80) REVERT: Q 166 ASN cc_start: 0.8437 (t0) cc_final: 0.8056 (t0) REVERT: R 186 GLU cc_start: 0.7661 (tt0) cc_final: 0.7042 (tm-30) REVERT: T 59 TYR cc_start: 0.8851 (t80) cc_final: 0.8535 (t80) REVERT: U 27 LEU cc_start: 0.7751 (tp) cc_final: 0.7362 (mt) REVERT: U 28 GLU cc_start: 0.7072 (pp20) cc_final: 0.6553 (pp20) REVERT: U 56 GLU cc_start: 0.7587 (tt0) cc_final: 0.7361 (mt-10) REVERT: V 70 LEU cc_start: 0.9115 (tp) cc_final: 0.8777 (tp) REVERT: W 18 SER cc_start: 0.8078 (p) cc_final: 0.7643 (t) REVERT: B 63 LEU cc_start: 0.9151 (mt) cc_final: 0.8849 (tp) REVERT: B 261 SER cc_start: 0.8109 (t) cc_final: 0.7853 (p) REVERT: C 44 GLN cc_start: 0.8507 (tt0) cc_final: 0.7817 (mm110) REVERT: C 96 MET cc_start: 0.8208 (mmt) cc_final: 0.7760 (mmm) REVERT: C 137 GLN cc_start: 0.7203 (tm-30) cc_final: 0.6810 (tm-30) REVERT: C 139 SER cc_start: 0.9189 (m) cc_final: 0.8965 (m) REVERT: C 214 ASP cc_start: 0.8355 (m-30) cc_final: 0.8124 (m-30) REVERT: C 240 MET cc_start: 0.8589 (mmp) cc_final: 0.8050 (mmt) REVERT: C 311 LYS cc_start: 0.9209 (mttm) cc_final: 0.8843 (mtpp) REVERT: C 323 CYS cc_start: 0.8342 (m) cc_final: 0.7974 (t) REVERT: D 43 MET cc_start: 0.8454 (tpp) cc_final: 0.8221 (tpp) REVERT: E 131 GLU cc_start: 0.7146 (pm20) cc_final: 0.5918 (tp30) REVERT: J 16 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7191 (tpt170) REVERT: J 18 SER cc_start: 0.8373 (p) cc_final: 0.8102 (p) REVERT: J 40 ASP cc_start: 0.6983 (m-30) cc_final: 0.6761 (m-30) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.7850 time to fit residues: 668.7233 Evaluate side-chains 401 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 366 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 ASN Q 200 HIS R 53 ASN R 57 GLN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN D 200 HIS ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 31772 Z= 0.285 Angle : 0.575 11.430 43226 Z= 0.291 Chirality : 0.045 1.457 4750 Planarity : 0.004 0.064 5514 Dihedral : 6.797 89.527 4322 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 3850 helix: -0.42 (0.12), residues: 1912 sheet: -2.23 (0.29), residues: 296 loop : -1.93 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 379 HIS 0.007 0.001 HIS Q 198 PHE 0.014 0.001 PHE P 183 TYR 0.025 0.002 TYR J 59 ARG 0.007 0.001 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 521 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 96 MET cc_start: 0.8357 (mmt) cc_final: 0.7936 (mmm) REVERT: P 311 LYS cc_start: 0.9226 (mttm) cc_final: 0.8967 (mtpp) REVERT: P 323 CYS cc_start: 0.8409 (m) cc_final: 0.8149 (t) REVERT: Q 22 ASP cc_start: 0.6805 (m-30) cc_final: 0.6529 (m-30) REVERT: Q 43 MET cc_start: 0.8602 (tpp) cc_final: 0.8354 (tpp) REVERT: Q 153 PHE cc_start: 0.8291 (t80) cc_final: 0.8030 (t80) REVERT: Q 166 ASN cc_start: 0.8430 (t0) cc_final: 0.8055 (t0) REVERT: Q 208 MET cc_start: 0.8496 (tmm) cc_final: 0.8211 (tmm) REVERT: T 38 LEU cc_start: 0.9014 (mt) cc_final: 0.8761 (tp) REVERT: U 27 LEU cc_start: 0.7764 (tp) cc_final: 0.7294 (mt) REVERT: U 28 GLU cc_start: 0.7140 (pp20) cc_final: 0.6602 (pp20) REVERT: U 56 GLU cc_start: 0.7606 (tt0) cc_final: 0.7385 (mt-10) REVERT: V 70 LEU cc_start: 0.9175 (tp) cc_final: 0.8825 (tp) REVERT: W 18 SER cc_start: 0.8005 (p) cc_final: 0.7611 (t) REVERT: W 40 ASP cc_start: 0.7253 (m-30) cc_final: 0.6888 (t0) REVERT: B 63 LEU cc_start: 0.9174 (mt) cc_final: 0.8859 (tp) REVERT: C 44 GLN cc_start: 0.8495 (tt0) cc_final: 0.7809 (mm110) REVERT: C 96 MET cc_start: 0.8247 (mmt) cc_final: 0.7795 (mmm) REVERT: C 214 ASP cc_start: 0.8382 (m-30) cc_final: 0.8147 (m-30) REVERT: C 311 LYS cc_start: 0.9206 (mttm) cc_final: 0.8941 (mttm) REVERT: C 323 CYS cc_start: 0.8349 (m) cc_final: 0.8023 (t) REVERT: D 43 MET cc_start: 0.8586 (tpp) cc_final: 0.8332 (tpp) REVERT: E 131 GLU cc_start: 0.7284 (pm20) cc_final: 0.5947 (tp30) REVERT: E 186 GLU cc_start: 0.7837 (tt0) cc_final: 0.6530 (mm-30) REVERT: F 41 ASP cc_start: 0.8554 (p0) cc_final: 0.8112 (p0) REVERT: J 16 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7221 (tpt170) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.7560 time to fit residues: 638.3718 Evaluate side-chains 411 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 232 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 ASN Q 75 ASN Q 200 HIS ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 31772 Z= 0.260 Angle : 0.562 11.432 43226 Z= 0.283 Chirality : 0.044 1.466 4750 Planarity : 0.004 0.058 5514 Dihedral : 6.698 89.568 4322 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 3850 helix: -0.26 (0.12), residues: 1912 sheet: -2.19 (0.28), residues: 296 loop : -1.83 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 379 HIS 0.006 0.001 HIS Q 198 PHE 0.026 0.001 PHE P 183 TYR 0.019 0.001 TYR W 59 ARG 0.006 0.000 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 528 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 18 PHE cc_start: 0.8810 (m-80) cc_final: 0.7487 (t80) REVERT: P 96 MET cc_start: 0.8415 (mmt) cc_final: 0.8026 (mmm) REVERT: P 139 SER cc_start: 0.9236 (m) cc_final: 0.8990 (m) REVERT: P 311 LYS cc_start: 0.9224 (mttm) cc_final: 0.8988 (mtpp) REVERT: Q 22 ASP cc_start: 0.6794 (m-30) cc_final: 0.6534 (m-30) REVERT: Q 43 MET cc_start: 0.8617 (tpp) cc_final: 0.8341 (tpp) REVERT: Q 153 PHE cc_start: 0.8311 (t80) cc_final: 0.8036 (t80) REVERT: Q 166 ASN cc_start: 0.8466 (t0) cc_final: 0.8118 (t0) REVERT: Q 208 MET cc_start: 0.8542 (tmm) cc_final: 0.8192 (tmm) REVERT: T 38 LEU cc_start: 0.9001 (mt) cc_final: 0.8760 (tp) REVERT: U 27 LEU cc_start: 0.7800 (tp) cc_final: 0.7316 (mt) REVERT: U 28 GLU cc_start: 0.7156 (pp20) cc_final: 0.6522 (pp20) REVERT: U 56 GLU cc_start: 0.7631 (tt0) cc_final: 0.7376 (mt-10) REVERT: V 70 LEU cc_start: 0.9203 (tp) cc_final: 0.8847 (tp) REVERT: W 18 SER cc_start: 0.7986 (p) cc_final: 0.7611 (t) REVERT: W 40 ASP cc_start: 0.7051 (m-30) cc_final: 0.6772 (t0) REVERT: B 63 LEU cc_start: 0.9242 (mt) cc_final: 0.8893 (tp) REVERT: B 146 ILE cc_start: 0.8748 (mm) cc_final: 0.8276 (tp) REVERT: C 18 PHE cc_start: 0.8818 (m-80) cc_final: 0.7392 (t80) REVERT: C 44 GLN cc_start: 0.8483 (tt0) cc_final: 0.7775 (mm110) REVERT: C 96 MET cc_start: 0.8196 (mmt) cc_final: 0.7724 (mmm) REVERT: C 139 SER cc_start: 0.9272 (m) cc_final: 0.9007 (m) REVERT: C 311 LYS cc_start: 0.9216 (mttm) cc_final: 0.8980 (mttm) REVERT: C 323 CYS cc_start: 0.8330 (m) cc_final: 0.8040 (t) REVERT: D 43 MET cc_start: 0.8631 (tpp) cc_final: 0.8259 (tpp) REVERT: E 131 GLU cc_start: 0.7316 (pm20) cc_final: 0.5947 (tp30) REVERT: E 186 GLU cc_start: 0.7852 (tt0) cc_final: 0.6589 (mm-30) REVERT: J 16 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7183 (tpt170) REVERT: J 18 SER cc_start: 0.8511 (p) cc_final: 0.8186 (p) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.7931 time to fit residues: 684.1031 Evaluate side-chains 423 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 chunk 341 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 308 optimal weight: 0.0060 chunk 322 optimal weight: 2.9990 chunk 340 optimal weight: 5.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 126 GLN ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 HIS ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 31772 Z= 0.212 Angle : 0.532 11.453 43226 Z= 0.267 Chirality : 0.044 1.479 4750 Planarity : 0.004 0.056 5514 Dihedral : 6.504 89.329 4322 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3850 helix: 0.01 (0.12), residues: 1910 sheet: -1.85 (0.30), residues: 274 loop : -1.73 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 379 HIS 0.004 0.001 HIS P 97 PHE 0.021 0.001 PHE P 183 TYR 0.030 0.001 TYR P 155 ARG 0.007 0.000 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 537 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 3.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 295 LEU cc_start: 0.8192 (tt) cc_final: 0.7986 (tt) REVERT: P 18 PHE cc_start: 0.8858 (m-80) cc_final: 0.7459 (t80) REVERT: P 96 MET cc_start: 0.8327 (mmt) cc_final: 0.8000 (mmm) REVERT: P 139 SER cc_start: 0.9259 (m) cc_final: 0.8961 (m) REVERT: P 240 MET cc_start: 0.8546 (mmp) cc_final: 0.7532 (mmt) REVERT: P 311 LYS cc_start: 0.9226 (mttm) cc_final: 0.8988 (mtpp) REVERT: Q 43 MET cc_start: 0.8596 (tpp) cc_final: 0.8303 (tpp) REVERT: Q 153 PHE cc_start: 0.8291 (t80) cc_final: 0.8002 (t80) REVERT: Q 166 ASN cc_start: 0.8439 (t0) cc_final: 0.8066 (t0) REVERT: Q 208 MET cc_start: 0.8469 (tmm) cc_final: 0.8116 (tmm) REVERT: T 38 LEU cc_start: 0.8981 (mt) cc_final: 0.8761 (tp) REVERT: U 27 LEU cc_start: 0.7799 (tp) cc_final: 0.7267 (mt) REVERT: U 28 GLU cc_start: 0.7092 (pp20) cc_final: 0.6787 (pp20) REVERT: U 56 GLU cc_start: 0.7619 (tt0) cc_final: 0.7342 (mt-10) REVERT: V 70 LEU cc_start: 0.9214 (tp) cc_final: 0.8841 (tp) REVERT: W 18 SER cc_start: 0.7957 (p) cc_final: 0.7562 (t) REVERT: B 55 SER cc_start: 0.8696 (p) cc_final: 0.8403 (t) REVERT: B 63 LEU cc_start: 0.9239 (mt) cc_final: 0.8856 (tp) REVERT: B 146 ILE cc_start: 0.8738 (mm) cc_final: 0.8277 (tp) REVERT: C 18 PHE cc_start: 0.8889 (m-80) cc_final: 0.7387 (t80) REVERT: C 44 GLN cc_start: 0.8397 (tt0) cc_final: 0.7764 (mm110) REVERT: C 96 MET cc_start: 0.8155 (mmt) cc_final: 0.7637 (mmm) REVERT: C 139 SER cc_start: 0.9278 (m) cc_final: 0.9003 (m) REVERT: C 311 LYS cc_start: 0.9200 (mttm) cc_final: 0.8960 (mttm) REVERT: C 323 CYS cc_start: 0.8267 (m) cc_final: 0.8036 (t) REVERT: D 43 MET cc_start: 0.8619 (tpp) cc_final: 0.8250 (tpp) REVERT: E 131 GLU cc_start: 0.7221 (pm20) cc_final: 0.5802 (tp30) REVERT: E 186 GLU cc_start: 0.7847 (tt0) cc_final: 0.6606 (mm-30) REVERT: J 16 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.7206 (tpt170) REVERT: J 18 SER cc_start: 0.8511 (p) cc_final: 0.8153 (p) outliers start: 0 outliers final: 0 residues processed: 537 average time/residue: 0.7678 time to fit residues: 674.6404 Evaluate side-chains 428 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 6.9990 chunk 360 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 250 optimal weight: 0.5980 chunk 378 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 85 HIS ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 ASN Q 75 ASN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 31772 Z= 0.248 Angle : 0.547 11.428 43226 Z= 0.275 Chirality : 0.044 1.466 4750 Planarity : 0.004 0.057 5514 Dihedral : 6.481 88.955 4322 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3850 helix: 0.09 (0.12), residues: 1906 sheet: -1.83 (0.30), residues: 274 loop : -1.70 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 379 HIS 0.006 0.001 HIS Q 198 PHE 0.016 0.001 PHE P 183 TYR 0.026 0.001 TYR P 155 ARG 0.006 0.000 ARG N 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Evaluate side-chains 529 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: P 18 PHE cc_start: 0.8883 (m-80) cc_final: 0.7546 (t80) REVERT: P 96 MET cc_start: 0.8329 (mmt) cc_final: 0.8005 (mmm) REVERT: P 139 SER cc_start: 0.9218 (m) cc_final: 0.8922 (m) REVERT: P 311 LYS cc_start: 0.9256 (mttm) cc_final: 0.9026 (mtpp) REVERT: Q 43 MET cc_start: 0.8609 (tpp) cc_final: 0.8350 (tpp) REVERT: Q 112 ASP cc_start: 0.8406 (t0) cc_final: 0.8206 (t70) REVERT: Q 153 PHE cc_start: 0.8304 (t80) cc_final: 0.8026 (t80) REVERT: Q 166 ASN cc_start: 0.8470 (t0) cc_final: 0.8099 (t0) REVERT: Q 208 MET cc_start: 0.8447 (tmm) cc_final: 0.8195 (tmm) REVERT: T 38 LEU cc_start: 0.8988 (mt) cc_final: 0.8769 (tp) REVERT: U 27 LEU cc_start: 0.7840 (tp) cc_final: 0.7281 (mt) REVERT: U 28 GLU cc_start: 0.7160 (pp20) cc_final: 0.6784 (pp20) REVERT: U 56 GLU cc_start: 0.7683 (tt0) cc_final: 0.7347 (mt-10) REVERT: V 70 LEU cc_start: 0.9211 (tp) cc_final: 0.8849 (tp) REVERT: B 63 LEU cc_start: 0.9246 (mt) cc_final: 0.8914 (tp) REVERT: B 146 ILE cc_start: 0.8717 (mm) cc_final: 0.8300 (tp) REVERT: C 18 PHE cc_start: 0.8841 (m-80) cc_final: 0.7391 (t80) REVERT: C 44 GLN cc_start: 0.8442 (tt0) cc_final: 0.7844 (mm110) REVERT: C 96 MET cc_start: 0.8178 (mmt) cc_final: 0.7647 (mmm) REVERT: C 139 SER cc_start: 0.9273 (m) cc_final: 0.9002 (m) REVERT: C 214 ASP cc_start: 0.8362 (m-30) cc_final: 0.8114 (m-30) REVERT: C 240 MET cc_start: 0.8650 (mmp) cc_final: 0.7812 (mmt) REVERT: C 311 LYS cc_start: 0.9217 (mttm) cc_final: 0.8965 (mttm) REVERT: D 43 MET cc_start: 0.8681 (tpp) cc_final: 0.8291 (tpp) REVERT: E 131 GLU cc_start: 0.7233 (pm20) cc_final: 0.5725 (tp30) REVERT: E 186 GLU cc_start: 0.7844 (tt0) cc_final: 0.6601 (mm-30) REVERT: J 16 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7215 (tpt170) REVERT: J 18 SER cc_start: 0.8476 (p) cc_final: 0.8148 (p) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.7723 time to fit residues: 670.4657 Evaluate side-chains 437 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 1.9990 chunk 321 optimal weight: 0.0980 chunk 92 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 301 optimal weight: 0.0970 chunk 126 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 ASN T 23 GLN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.094617 restraints weight = 179578.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097957 restraints weight = 77387.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099954 restraints weight = 41627.565| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 31772 Z= 0.160 Angle : 0.513 11.438 43226 Z= 0.256 Chirality : 0.044 1.501 4750 Planarity : 0.004 0.051 5514 Dihedral : 6.284 87.468 4322 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -0.90 (0.14), residues: 3850 helix: 0.33 (0.12), residues: 1906 sheet: -1.86 (0.28), residues: 292 loop : -1.40 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 379 HIS 0.005 0.001 HIS P 97 PHE 0.024 0.001 PHE P 183 TYR 0.030 0.001 TYR C 155 ARG 0.011 0.000 ARG C 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12133.60 seconds wall clock time: 211 minutes 12.26 seconds (12672.26 seconds total)