Starting phenix.real_space_refine on Sun Mar 17 22:21:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/03_2024/7xlb_33276.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/03_2024/7xlb_33276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/03_2024/7xlb_33276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/03_2024/7xlb_33276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/03_2024/7xlb_33276.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/03_2024/7xlb_33276.pdb" } resolution = 3.44 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= 0.007 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 12404 2.51 5 N 3304 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 120": "OE1" <-> "OE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C ASP 372": "OD1" <-> "OD2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "F TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 370": "OE1" <-> "OE2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 370": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19138 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "F" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Chain: "G" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2734 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 321} Chain breaks: 3 Time building chain proxies: 10.31, per 1000 atoms: 0.54 Number of scatterers: 19138 At special positions: 0 Unit cell: (126.96, 126.96, 129.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3346 8.00 N 3304 7.00 C 12404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 279 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 279 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 259 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 279 " distance=2.03 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 259 " distance=2.03 Simple disulfide: pdb=" SG CYS G 81 " - pdb=" SG CYS G 279 " distance=2.03 Simple disulfide: pdb=" SG CYS G 99 " - pdb=" SG CYS G 259 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.61 Conformation dependent library (CDL) restraints added in 3.3 seconds 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 7 sheets defined 60.4% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 59 through 65 removed outlier: 3.808A pdb=" N ILE E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 90 through 99 removed outlier: 3.934A pdb=" N TYR E 94 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 95 " --> pdb=" O GLN E 91 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 removed outlier: 4.143A pdb=" N LYS E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 144 removed outlier: 4.375A pdb=" N TRP E 142 " --> pdb=" O PRO E 138 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.681A pdb=" N PHE E 156 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 157 " --> pdb=" O GLU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.584A pdb=" N GLN E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER E 182 " --> pdb=" O LYS E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 182' Processing helix chain 'E' and resid 191 through 198 removed outlier: 4.143A pdb=" N ASN E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 208 removed outlier: 4.309A pdb=" N ASN E 208 " --> pdb=" O PRO E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 218 Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.764A pdb=" N LEU E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 239 through 252 removed outlier: 3.837A pdb=" N LEU E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS E 246 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR E 247 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR E 248 " --> pdb=" O TYR E 244 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR E 249 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 250 " --> pdb=" O CYS E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 292 through 300 removed outlier: 4.027A pdb=" N VAL E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 315 removed outlier: 3.753A pdb=" N ILE E 304 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 305 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 306 " --> pdb=" O ASN E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 327 removed outlier: 4.366A pdb=" N LYS E 327 " --> pdb=" O LYS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 removed outlier: 4.120A pdb=" N ILE E 346 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 350 " --> pdb=" O ILE E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 369 removed outlier: 3.677A pdb=" N ASN E 369 " --> pdb=" O ASP E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 372 No H-bonds generated for 'chain 'E' and resid 370 through 372' Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.734A pdb=" N LEU E 382 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 383 " --> pdb=" O VAL E 379 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.764A pdb=" N ILE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.922A pdb=" N TYR A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 124 removed outlier: 4.112A pdb=" N LYS A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 4.370A pdb=" N TRP A 142 " --> pdb=" O PRO A 138 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.682A pdb=" N PHE A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.583A pdb=" N GLN A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 182' Processing helix chain 'A' and resid 191 through 198 removed outlier: 4.143A pdb=" N ASN A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 4.307A pdb=" N ASN A 208 " --> pdb=" O PRO A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.712A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.788A pdb=" N LEU A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 248 " --> pdb=" O TYR A 244 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 250 " --> pdb=" O CYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 292 through 300 removed outlier: 4.044A pdb=" N VAL A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.758A pdb=" N ILE A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 4.305A pdb=" N LYS A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 4.097A pdb=" N ILE A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.630A pdb=" N ASN A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 378 through 386 removed outlier: 3.734A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.776A pdb=" N ILE B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.939A pdb=" N TYR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 4.138A pdb=" N LYS B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 144 removed outlier: 4.372A pdb=" N TRP B 142 " --> pdb=" O PRO B 138 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 removed outlier: 3.711A pdb=" N PHE B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.584A pdb=" N GLN B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 182' Processing helix chain 'B' and resid 191 through 198 removed outlier: 4.142A pdb=" N ASN B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 4.310A pdb=" N ASN B 208 " --> pdb=" O PRO B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.718A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 239 through 252 removed outlier: 3.839A pdb=" N LEU B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 248 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 250 " --> pdb=" O CYS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 292 through 300 removed outlier: 4.057A pdb=" N VAL B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 315 removed outlier: 3.761A pdb=" N ILE B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 305 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 removed outlier: 4.283A pdb=" N LYS B 327 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 4.081A pdb=" N ILE B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 removed outlier: 3.632A pdb=" N ASN B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 378 through 386 removed outlier: 3.737A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 59 Processing helix chain 'C' and resid 59 through 65 removed outlier: 3.766A pdb=" N ILE C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.940A pdb=" N TYR C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA C 95 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 124 removed outlier: 4.136A pdb=" N LYS C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 144 removed outlier: 4.374A pdb=" N TRP C 142 " --> pdb=" O PRO C 138 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.676A pdb=" N PHE C 156 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.585A pdb=" N GLN C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 182' Processing helix chain 'C' and resid 191 through 198 removed outlier: 4.141A pdb=" N ASN C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 removed outlier: 4.309A pdb=" N ASN C 208 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.720A pdb=" N LEU C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA C 229 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 239 through 252 removed outlier: 3.796A pdb=" N LEU C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS C 246 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 248 " --> pdb=" O TYR C 244 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 250 " --> pdb=" O CYS C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 292 through 300 removed outlier: 4.033A pdb=" N VAL C 296 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.731A pdb=" N ILE C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 305 " --> pdb=" O MET C 301 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 removed outlier: 4.289A pdb=" N LYS C 327 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 4.107A pdb=" N ILE C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 350 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 369 removed outlier: 3.626A pdb=" N ASN C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 378 through 386 removed outlier: 3.735A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 59 through 65 removed outlier: 3.783A pdb=" N ILE D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 74 Processing helix chain 'D' and resid 90 through 99 removed outlier: 3.932A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 124 removed outlier: 4.143A pdb=" N LYS D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 144 removed outlier: 4.200A pdb=" N TRP D 142 " --> pdb=" O PRO D 138 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 removed outlier: 3.699A pdb=" N PHE D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 177 through 182 removed outlier: 3.585A pdb=" N GLN D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 182' Processing helix chain 'D' and resid 191 through 198 removed outlier: 4.142A pdb=" N ASN D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 removed outlier: 4.309A pdb=" N ASN D 208 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.730A pdb=" N LEU D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA D 229 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 239 through 252 removed outlier: 3.816A pdb=" N LEU D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS D 246 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 248 " --> pdb=" O TYR D 244 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 250 " --> pdb=" O CYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 292 through 300 removed outlier: 4.043A pdb=" N VAL D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 315 removed outlier: 3.752A pdb=" N ILE D 304 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 305 " --> pdb=" O MET D 301 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 removed outlier: 4.352A pdb=" N LYS D 327 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 4.100A pdb=" N ILE D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 350 " --> pdb=" O ILE D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 369 removed outlier: 3.666A pdb=" N ASN D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 378 through 386 removed outlier: 3.731A pdb=" N LEU D 382 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 383 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 59 Processing helix chain 'F' and resid 59 through 65 removed outlier: 3.811A pdb=" N ILE F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 90 through 99 removed outlier: 3.936A pdb=" N TYR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 95 " --> pdb=" O GLN F 91 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS F 99 " --> pdb=" O ALA F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 124 removed outlier: 4.140A pdb=" N LYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 144 removed outlier: 4.167A pdb=" N TRP F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 160 removed outlier: 3.665A pdb=" N PHE F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU F 157 " --> pdb=" O GLU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.582A pdb=" N GLN F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER F 182 " --> pdb=" O LYS F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 182' Processing helix chain 'F' and resid 191 through 198 removed outlier: 4.143A pdb=" N ASN F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 208 removed outlier: 4.310A pdb=" N ASN F 208 " --> pdb=" O PRO F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 218 Processing helix chain 'F' and resid 223 through 238 removed outlier: 3.672A pdb=" N LEU F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 233 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE F 234 " --> pdb=" O ARG F 230 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 236 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 252 removed outlier: 3.808A pdb=" N LEU F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS F 246 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR F 247 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR F 249 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA F 250 " --> pdb=" O CYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 292 through 300 removed outlier: 4.043A pdb=" N VAL F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 315 removed outlier: 3.752A pdb=" N ILE F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 305 " --> pdb=" O MET F 301 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU F 306 " --> pdb=" O ASN F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 327 removed outlier: 4.291A pdb=" N LYS F 327 " --> pdb=" O LYS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 354 removed outlier: 4.116A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 removed outlier: 3.654A pdb=" N ASN F 369 " --> pdb=" O ASP F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 378 through 386 removed outlier: 3.732A pdb=" N LEU F 382 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 383 " --> pdb=" O VAL F 379 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 59 Processing helix chain 'G' and resid 59 through 65 removed outlier: 3.786A pdb=" N ILE G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 Processing helix chain 'G' and resid 90 through 99 removed outlier: 3.917A pdb=" N TYR G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 95 " --> pdb=" O GLN G 91 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 124 removed outlier: 4.157A pdb=" N LYS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 144 removed outlier: 4.223A pdb=" N TRP G 142 " --> pdb=" O PRO G 138 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE G 144 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 160 removed outlier: 3.711A pdb=" N PHE G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU G 157 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 177 through 182 removed outlier: 3.582A pdb=" N GLN G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER G 182 " --> pdb=" O LYS G 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 177 through 182' Processing helix chain 'G' and resid 191 through 198 removed outlier: 4.140A pdb=" N ASN G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 208 removed outlier: 4.310A pdb=" N ASN G 208 " --> pdb=" O PRO G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 218 Processing helix chain 'G' and resid 223 through 233 removed outlier: 3.740A pdb=" N LEU G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA G 229 " --> pdb=" O LYS G 225 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 239 through 252 removed outlier: 3.848A pdb=" N LEU G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 246 " --> pdb=" O ILE G 242 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR G 247 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR G 248 " --> pdb=" O TYR G 244 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR G 249 " --> pdb=" O LEU G 245 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 250 " --> pdb=" O CYS G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 292 through 300 removed outlier: 4.037A pdb=" N VAL G 296 " --> pdb=" O GLY G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 315 removed outlier: 3.761A pdb=" N ILE G 304 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE G 305 " --> pdb=" O MET G 301 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 306 " --> pdb=" O ASN G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 327 removed outlier: 4.296A pdb=" N LYS G 327 " --> pdb=" O LYS G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 4.089A pdb=" N ILE G 346 " --> pdb=" O CYS G 342 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE G 350 " --> pdb=" O ILE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 369 removed outlier: 3.615A pdb=" N ASN G 369 " --> pdb=" O ASP G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 372 No H-bonds generated for 'chain 'G' and resid 370 through 372' Processing helix chain 'G' and resid 378 through 386 removed outlier: 3.732A pdb=" N LEU G 382 " --> pdb=" O VAL G 378 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 383 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 589 hydrogen bonds defined for protein. 1662 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: 4.72 Time building geometry restraints manager: 8.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6146 1.35 - 1.46: 4421 1.46 - 1.58: 8855 1.58 - 1.70: 3 1.70 - 1.82: 105 Bond restraints: 19530 Sorted by residual: bond pdb=" CB PRO B 125 " pdb=" CG PRO B 125 " ideal model delta sigma weight residual 1.492 1.632 -0.140 5.00e-02 4.00e+02 7.89e+00 bond pdb=" CB PRO C 125 " pdb=" CG PRO C 125 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.09e+00 bond pdb=" CB PRO G 125 " pdb=" CG PRO G 125 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.00e+00 bond pdb=" N PRO B 125 " pdb=" CA PRO B 125 " ideal model delta sigma weight residual 1.471 1.445 0.025 1.32e-02 5.74e+03 3.67e+00 bond pdb=" N PRO C 125 " pdb=" CA PRO C 125 " ideal model delta sigma weight residual 1.472 1.448 0.024 1.32e-02 5.74e+03 3.29e+00 ... (remaining 19525 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.47: 346 105.47 - 112.61: 9875 112.61 - 119.75: 7234 119.75 - 126.90: 8766 126.90 - 134.04: 211 Bond angle restraints: 26432 Sorted by residual: angle pdb=" CA PRO B 125 " pdb=" N PRO B 125 " pdb=" CD PRO B 125 " ideal model delta sigma weight residual 112.00 98.65 13.35 1.40e+00 5.10e-01 9.09e+01 angle pdb=" CA PRO C 125 " pdb=" N PRO C 125 " pdb=" CD PRO C 125 " ideal model delta sigma weight residual 112.00 99.88 12.12 1.40e+00 5.10e-01 7.49e+01 angle pdb=" CA PRO G 125 " pdb=" N PRO G 125 " pdb=" CD PRO G 125 " ideal model delta sigma weight residual 112.00 102.22 9.78 1.40e+00 5.10e-01 4.88e+01 angle pdb=" CA PRO B 62 " pdb=" N PRO B 62 " pdb=" CD PRO B 62 " ideal model delta sigma weight residual 112.00 103.51 8.49 1.40e+00 5.10e-01 3.68e+01 angle pdb=" CA PRO F 62 " pdb=" N PRO F 62 " pdb=" CD PRO F 62 " ideal model delta sigma weight residual 112.00 103.58 8.42 1.40e+00 5.10e-01 3.62e+01 ... (remaining 26427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 9686 17.66 - 35.33: 1547 35.33 - 52.99: 563 52.99 - 70.65: 49 70.65 - 88.31: 41 Dihedral angle restraints: 11886 sinusoidal: 4914 harmonic: 6972 Sorted by residual: dihedral pdb=" CA LEU D 124 " pdb=" C LEU D 124 " pdb=" N PRO D 125 " pdb=" CA PRO D 125 " ideal model delta harmonic sigma weight residual 180.00 139.07 40.93 0 5.00e+00 4.00e-02 6.70e+01 dihedral pdb=" CA LEU F 124 " pdb=" C LEU F 124 " pdb=" N PRO F 125 " pdb=" CA PRO F 125 " ideal model delta harmonic sigma weight residual 180.00 139.81 40.19 0 5.00e+00 4.00e-02 6.46e+01 dihedral pdb=" CA LEU E 124 " pdb=" C LEU E 124 " pdb=" N PRO E 125 " pdb=" CA PRO E 125 " ideal model delta harmonic sigma weight residual 180.00 139.85 40.15 0 5.00e+00 4.00e-02 6.45e+01 ... (remaining 11883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1858 0.030 - 0.060: 883 0.060 - 0.091: 198 0.091 - 0.121: 82 0.121 - 0.151: 24 Chirality restraints: 3045 Sorted by residual: chirality pdb=" CB THR D 151 " pdb=" CA THR D 151 " pdb=" OG1 THR D 151 " pdb=" CG2 THR D 151 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CB THR C 151 " pdb=" CA THR C 151 " pdb=" OG1 THR C 151 " pdb=" CG2 THR C 151 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE G 289 " pdb=" N ILE G 289 " pdb=" C ILE G 289 " pdb=" CB ILE G 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 3042 not shown) Planarity restraints: 3325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 124 " 0.126 5.00e-02 4.00e+02 1.80e-01 5.20e+01 pdb=" N PRO B 125 " -0.311 5.00e-02 4.00e+02 pdb=" CA PRO B 125 " 0.097 5.00e-02 4.00e+02 pdb=" CD PRO B 125 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 124 " 0.122 5.00e-02 4.00e+02 1.75e-01 4.92e+01 pdb=" N PRO C 125 " -0.303 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 124 " -0.116 5.00e-02 4.00e+02 1.69e-01 4.58e+01 pdb=" N PRO G 125 " 0.292 5.00e-02 4.00e+02 pdb=" CA PRO G 125 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO G 125 " -0.084 5.00e-02 4.00e+02 ... (remaining 3322 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3408 2.77 - 3.30: 17309 3.30 - 3.83: 29189 3.83 - 4.37: 32769 4.37 - 4.90: 56333 Nonbonded interactions: 139008 Sorted by model distance: nonbonded pdb=" OD1 ASP A 365 " pdb=" ND2 ASN A 369 " model vdw 2.236 2.520 nonbonded pdb=" OD1 ASP B 365 " pdb=" ND2 ASN B 369 " model vdw 2.242 2.520 nonbonded pdb=" NH1 ARG E 363 " pdb=" OE2 GLU G 160 " model vdw 2.244 2.520 nonbonded pdb=" OD1 ASP C 365 " pdb=" ND2 ASN C 369 " model vdw 2.245 2.520 nonbonded pdb=" OD1 ASP G 365 " pdb=" ND2 ASN G 369 " model vdw 2.245 2.520 ... (remaining 139003 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.120 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 48.980 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 19530 Z= 0.192 Angle : 0.640 13.350 26432 Z= 0.357 Chirality : 0.038 0.151 3045 Planarity : 0.011 0.180 3325 Dihedral : 19.227 88.312 7280 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.19 % Allowed : 37.84 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.68 (0.16), residues: 2296 helix: -2.54 (0.14), residues: 1281 sheet: -0.54 (0.54), residues: 105 loop : -2.30 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 115 HIS 0.003 0.000 HIS B 326 PHE 0.019 0.001 PHE A 366 TYR 0.016 0.001 TYR F 165 ARG 0.004 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 2.226 Fit side-chains REVERT: A 135 MET cc_start: 0.7532 (mmt) cc_final: 0.6643 (mmt) outliers start: 4 outliers final: 0 residues processed: 128 average time/residue: 0.2840 time to fit residues: 58.6463 Evaluate side-chains 110 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN A 155 ASN B 155 ASN B 252 GLN C 155 ASN C 252 GLN D 155 ASN ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN F 319 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19530 Z= 0.406 Angle : 0.771 12.807 26432 Z= 0.390 Chirality : 0.047 0.166 3045 Planarity : 0.009 0.138 3325 Dihedral : 5.627 39.093 2569 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 8.07 % Allowed : 32.49 % Favored : 59.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.79 (0.16), residues: 2296 helix: -2.45 (0.13), residues: 1351 sheet: -1.58 (0.43), residues: 147 loop : -2.47 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 100 HIS 0.002 0.001 HIS C 121 PHE 0.024 0.002 PHE E 257 TYR 0.028 0.003 TYR D 82 ARG 0.006 0.001 ARG F 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 109 time to evaluate : 2.369 Fit side-chains revert: symmetry clash REVERT: A 234 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8016 (tt) REVERT: D 234 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7811 (tt) outliers start: 169 outliers final: 138 residues processed: 265 average time/residue: 0.2578 time to fit residues: 110.9085 Evaluate side-chains 242 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 102 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 311 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 HIS A 231 HIS B 155 ASN B 231 HIS C 231 HIS D 231 HIS G 231 HIS G 319 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19530 Z= 0.194 Angle : 0.629 10.667 26432 Z= 0.317 Chirality : 0.040 0.146 3045 Planarity : 0.007 0.117 3325 Dihedral : 5.375 38.336 2569 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 5.92 % Allowed : 35.07 % Favored : 59.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.49 (0.17), residues: 2296 helix: -2.26 (0.14), residues: 1330 sheet: -1.08 (0.54), residues: 112 loop : -2.33 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 100 HIS 0.002 0.000 HIS B 326 PHE 0.010 0.001 PHE E 257 TYR 0.016 0.002 TYR G 82 ARG 0.002 0.000 ARG F 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 115 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 223 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5652 (mp) REVERT: C 234 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7403 (tt) REVERT: C 349 MET cc_start: 0.7375 (mtt) cc_final: 0.6689 (mtt) REVERT: D 234 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7696 (tt) REVERT: F 245 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8153 (pp) REVERT: G 234 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7521 (tt) outliers start: 124 outliers final: 83 residues processed: 227 average time/residue: 0.2686 time to fit residues: 97.2406 Evaluate side-chains 190 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 102 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 320 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.0070 chunk 158 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 210 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN E 231 HIS A 155 ASN A 231 HIS B 155 ASN B 231 HIS C 155 ASN C 231 HIS D 155 ASN D 231 HIS F 155 ASN G 231 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19530 Z= 0.181 Angle : 0.624 11.279 26432 Z= 0.312 Chirality : 0.040 0.144 3045 Planarity : 0.006 0.105 3325 Dihedral : 5.251 37.938 2569 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 7.26 % Allowed : 34.16 % Favored : 58.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.41 (0.17), residues: 2296 helix: -2.14 (0.14), residues: 1316 sheet: -1.15 (0.53), residues: 112 loop : -2.39 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 100 HIS 0.003 0.001 HIS A 231 PHE 0.008 0.001 PHE A 257 TYR 0.013 0.001 TYR G 82 ARG 0.003 0.000 ARG E 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 116 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7744 (tt) REVERT: C 234 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7395 (tt) REVERT: C 349 MET cc_start: 0.7385 (mtt) cc_final: 0.6687 (mtt) REVERT: D 128 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7988 (mp) REVERT: D 223 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5533 (mp) REVERT: F 234 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7762 (tt) REVERT: F 245 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8211 (pp) outliers start: 152 outliers final: 111 residues processed: 254 average time/residue: 0.2637 time to fit residues: 107.7049 Evaluate side-chains 226 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 109 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 320 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 154 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 200 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 HIS A 155 ASN A 231 HIS B 155 ASN B 231 HIS C 231 HIS D 231 HIS F 155 ASN G 231 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19530 Z= 0.163 Angle : 0.620 13.808 26432 Z= 0.305 Chirality : 0.040 0.214 3045 Planarity : 0.006 0.097 3325 Dihedral : 5.127 37.880 2569 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 6.93 % Allowed : 34.35 % Favored : 58.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.38 (0.17), residues: 2296 helix: -2.10 (0.14), residues: 1316 sheet: -1.14 (0.53), residues: 112 loop : -2.38 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 100 HIS 0.003 0.001 HIS A 231 PHE 0.014 0.001 PHE A 123 TYR 0.011 0.001 TYR G 82 ARG 0.003 0.000 ARG E 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 121 time to evaluate : 2.135 Fit side-chains revert: symmetry clash REVERT: A 234 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7712 (tt) REVERT: C 234 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7364 (tt) REVERT: C 349 MET cc_start: 0.7317 (mtt) cc_final: 0.6607 (mtt) REVERT: D 128 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7940 (mp) REVERT: D 223 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5526 (mp) REVERT: D 234 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7677 (tt) REVERT: F 234 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7768 (tt) REVERT: F 245 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8147 (pp) REVERT: G 234 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7428 (tt) outliers start: 145 outliers final: 108 residues processed: 254 average time/residue: 0.2579 time to fit residues: 104.7834 Evaluate side-chains 234 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 118 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 0.0170 chunk 55 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 155 ASN E 231 HIS A 155 ASN A 231 HIS B 155 ASN B 231 HIS C 155 ASN C 231 HIS D 231 HIS G 231 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19530 Z= 0.166 Angle : 0.618 14.169 26432 Z= 0.304 Chirality : 0.040 0.150 3045 Planarity : 0.005 0.092 3325 Dihedral : 5.054 37.814 2569 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 7.45 % Allowed : 34.16 % Favored : 58.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.33 (0.17), residues: 2296 helix: -2.06 (0.14), residues: 1316 sheet: -1.17 (0.52), residues: 112 loop : -2.36 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 100 HIS 0.003 0.001 HIS G 231 PHE 0.013 0.001 PHE G 320 TYR 0.011 0.001 TYR G 82 ARG 0.003 0.000 ARG E 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 122 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7925 (mp) REVERT: A 234 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7738 (tt) REVERT: C 234 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7439 (tt) REVERT: C 349 MET cc_start: 0.7293 (mtt) cc_final: 0.6592 (mtt) REVERT: D 128 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.7957 (mp) REVERT: D 223 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5512 (mp) REVERT: D 234 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7655 (tt) REVERT: F 234 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7754 (tt) REVERT: F 245 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8185 (pp) outliers start: 156 outliers final: 118 residues processed: 264 average time/residue: 0.2549 time to fit residues: 109.0286 Evaluate side-chains 246 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 120 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 127 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 188 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 chunk 222 optimal weight: 0.4980 chunk 139 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 HIS A 91 GLN A 155 ASN A 231 HIS B 155 ASN C 155 ASN C 231 HIS G 231 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19530 Z= 0.156 Angle : 0.618 14.496 26432 Z= 0.300 Chirality : 0.039 0.144 3045 Planarity : 0.005 0.088 3325 Dihedral : 4.966 37.672 2569 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 6.78 % Allowed : 35.12 % Favored : 58.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.26 (0.17), residues: 2296 helix: -2.00 (0.14), residues: 1316 sheet: -1.16 (0.52), residues: 112 loop : -2.33 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 100 HIS 0.004 0.001 HIS A 231 PHE 0.014 0.001 PHE F 320 TYR 0.009 0.001 TYR G 82 ARG 0.002 0.000 ARG E 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 124 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7677 (tt) REVERT: C 234 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7413 (tt) REVERT: C 349 MET cc_start: 0.7269 (mtt) cc_final: 0.6553 (mtt) REVERT: D 128 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.7973 (mp) REVERT: D 223 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5485 (mp) REVERT: F 234 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7695 (tt) REVERT: F 245 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8125 (pp) outliers start: 142 outliers final: 111 residues processed: 251 average time/residue: 0.2413 time to fit residues: 98.0794 Evaluate side-chains 241 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 124 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 0.0060 chunk 132 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 151 optimal weight: 0.4980 chunk 110 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 HIS D 231 HIS F 91 GLN G 231 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19530 Z= 0.153 Angle : 0.613 14.795 26432 Z= 0.297 Chirality : 0.039 0.145 3045 Planarity : 0.005 0.086 3325 Dihedral : 4.879 37.346 2569 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 6.50 % Allowed : 35.40 % Favored : 58.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.18 (0.17), residues: 2296 helix: -1.93 (0.15), residues: 1316 sheet: -1.17 (0.52), residues: 112 loop : -2.30 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 100 HIS 0.006 0.001 HIS G 231 PHE 0.013 0.001 PHE F 320 TYR 0.009 0.001 TYR A 82 ARG 0.004 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 127 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7968 (mp) REVERT: A 234 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7653 (tt) REVERT: C 234 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7399 (tt) REVERT: C 349 MET cc_start: 0.7247 (mtt) cc_final: 0.6535 (mtt) REVERT: D 128 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.7966 (mp) REVERT: D 223 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5493 (mp) REVERT: D 234 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7621 (tt) REVERT: F 234 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7632 (tt) REVERT: F 245 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8138 (pp) outliers start: 136 outliers final: 111 residues processed: 251 average time/residue: 0.2548 time to fit residues: 103.1766 Evaluate side-chains 243 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 124 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 207 optimal weight: 0.0040 chunk 124 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 206 optimal weight: 0.6980 chunk 136 optimal weight: 0.0870 overall best weight: 0.5972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 HIS A 155 ASN A 231 HIS B 91 GLN C 155 ASN C 231 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19530 Z= 0.155 Angle : 0.616 15.391 26432 Z= 0.295 Chirality : 0.039 0.145 3045 Planarity : 0.005 0.084 3325 Dihedral : 4.844 37.055 2569 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 6.69 % Allowed : 35.36 % Favored : 57.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.09 (0.17), residues: 2296 helix: -1.84 (0.15), residues: 1316 sheet: -1.15 (0.52), residues: 112 loop : -2.29 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 100 HIS 0.003 0.000 HIS D 231 PHE 0.011 0.001 PHE F 320 TYR 0.009 0.001 TYR G 82 ARG 0.003 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 126 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 234 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7621 (tt) REVERT: C 234 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7402 (tt) REVERT: C 349 MET cc_start: 0.7252 (mtt) cc_final: 0.6553 (mtt) REVERT: D 128 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.7994 (mp) REVERT: D 223 LEU cc_start: 0.5789 (OUTLIER) cc_final: 0.5491 (mp) REVERT: D 234 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7595 (tt) REVERT: F 234 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7624 (tt) REVERT: F 245 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8129 (pp) outliers start: 140 outliers final: 120 residues processed: 252 average time/residue: 0.2512 time to fit residues: 103.4982 Evaluate side-chains 251 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 123 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 230 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 155 ASN C 155 ASN C 231 HIS D 231 HIS F 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19530 Z= 0.231 Angle : 0.670 14.889 26432 Z= 0.322 Chirality : 0.041 0.139 3045 Planarity : 0.005 0.090 3325 Dihedral : 5.029 36.305 2569 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 6.21 % Allowed : 35.83 % Favored : 57.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.20 (0.17), residues: 2296 helix: -1.90 (0.15), residues: 1316 sheet: -1.35 (0.50), residues: 112 loop : -2.39 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 100 HIS 0.008 0.001 HIS C 231 PHE 0.013 0.001 PHE F 320 TYR 0.017 0.002 TYR G 82 ARG 0.002 0.000 ARG F 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4592 Ramachandran restraints generated. 2296 Oldfield, 0 Emsley, 2296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 118 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7722 (tt) REVERT: C 349 MET cc_start: 0.7358 (mtt) cc_final: 0.6660 (mtt) REVERT: D 128 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8059 (mp) REVERT: D 223 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5460 (mp) REVERT: D 234 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7695 (tt) REVERT: F 234 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7810 (tt) outliers start: 130 outliers final: 119 residues processed: 233 average time/residue: 0.2486 time to fit residues: 94.6128 Evaluate side-chains 242 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 118 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 TYR Chi-restraints excluded: chain E residue 164 CYS Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 TYR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 136 TYR Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 136 TYR Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 TYR Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 164 CYS Chi-restraints excluded: chain G residue 166 HIS Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 76 optimal weight: 0.0370 chunk 188 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 155 ASN C 91 GLN C 155 ASN C 231 HIS F 91 GLN G 91 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.226111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.208450 restraints weight = 22796.496| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 0.83 r_work: 0.4195 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work: 0.4072 rms_B_bonded: 3.50 restraints_weight: 0.1250 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19530 Z= 0.159 Angle : 0.628 15.811 26432 Z= 0.301 Chirality : 0.039 0.141 3045 Planarity : 0.005 0.111 3325 Dihedral : 4.940 37.206 2569 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 6.12 % Allowed : 36.07 % Favored : 57.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -3.13 (0.17), residues: 2296 helix: -1.84 (0.15), residues: 1316 sheet: -1.22 (0.52), residues: 112 loop : -2.36 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 100 HIS 0.004 0.000 HIS C 231 PHE 0.011 0.001 PHE F 320 TYR 0.011 0.001 TYR G 82 ARG 0.002 0.000 ARG A 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3550.68 seconds wall clock time: 69 minutes 0.06 seconds (4140.06 seconds total)