Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 9 13:55:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/10_2023/7xlb_33276.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/10_2023/7xlb_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_33276/10_2023/7xlb_33276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/10_2023/7xlb_33276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/10_2023/7xlb_33276.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xlb_33276/10_2023/7xlb_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 10.14, per 1000 atoms: 0.53 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: 6.98 Conformation dependent library (CDL) restraints added in 2.7 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: 1.93 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: 4.61 Time building geometry restraints manager: 7.50 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: 1.140 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: 6.010 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 46.930 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.100 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.450 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.182 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 128 average time/residue: 0.2933 time to fit residues: 60.4460 Evaluate side-chains 110 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.257 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0745 ------------------------------------------------------------------------------- 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: 0.7099 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19530 Z= 0.408 Angle : 0.761 12.613 26432 Z= 0.386 Chirality : 0.046 0.163 3045 Planarity : 0.009 0.136 3325 Dihedral : 5.604 39.131 2569 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 7.98 % Allowed : 32.63 % Favored : 59.39 % 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: -3.74 (0.16), residues: 2296 helix: -2.46 (0.13), residues: 1351 sheet: -1.34 (0.51), residues: 112 loop : -2.39 (0.20), residues: 833 *********************** 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: 167 poor density : 111 time to evaluate : 2.101 Fit side-chains revert: symmetry clash outliers start: 167 outliers final: 136 residues processed: 265 average time/residue: 0.2638 time to fit residues: 112.9137 Evaluate side-chains 239 residues out of total 2093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 103 time to evaluate : 2.083 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 0 residues processed: 136 average time/residue: 0.1644 time to fit residues: 45.2553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7786 > 50: distance: 5 - 20: 30.672 distance: 10 - 28: 29.189 distance: 17 - 20: 30.600 distance: 20 - 21: 40.497 distance: 21 - 22: 39.213 distance: 21 - 24: 20.624 distance: 22 - 23: 39.745 distance: 22 - 28: 56.381 distance: 24 - 25: 35.886 distance: 25 - 26: 20.331 distance: 25 - 27: 35.715 distance: 28 - 29: 21.971 distance: 29 - 30: 52.585 distance: 30 - 31: 40.997 distance: 30 - 32: 12.751 distance: 32 - 33: 47.878 distance: 33 - 34: 44.131 distance: 33 - 36: 40.302 distance: 34 - 35: 20.902 distance: 34 - 46: 34.502 distance: 36 - 37: 69.226 distance: 37 - 38: 36.864 distance: 37 - 39: 18.178 distance: 38 - 40: 19.883 distance: 39 - 41: 24.085 distance: 39 - 42: 36.349 distance: 40 - 41: 19.297 distance: 41 - 43: 26.538 distance: 42 - 44: 8.634 distance: 43 - 45: 26.263 distance: 44 - 45: 31.537 distance: 46 - 47: 18.672 distance: 47 - 48: 50.633 distance: 47 - 50: 32.124 distance: 48 - 49: 41.015 distance: 48 - 55: 20.529 distance: 50 - 51: 34.411 distance: 51 - 52: 41.071 distance: 52 - 53: 40.638 distance: 52 - 54: 4.899 distance: 55 - 56: 61.469 distance: 56 - 57: 40.716 distance: 57 - 58: 40.059 distance: 59 - 60: 13.517 distance: 60 - 61: 16.515 distance: 60 - 62: 19.654 distance: 61 - 63: 6.625 distance: 62 - 64: 39.923 distance: 63 - 65: 28.303 distance: 64 - 65: 18.158 distance: 66 - 67: 39.439 distance: 67 - 68: 40.416 distance: 67 - 70: 50.279 distance: 68 - 69: 56.705 distance: 68 - 74: 39.716 distance: 70 - 71: 37.438 distance: 71 - 72: 40.853 distance: 71 - 73: 40.906 distance: 74 - 75: 56.635 distance: 75 - 76: 40.085 distance: 75 - 78: 38.718 distance: 76 - 79: 69.048 distance: 79 - 80: 40.706 distance: 80 - 83: 45.231 distance: 81 - 82: 39.978 distance: 81 - 85: 57.615 distance: 83 - 84: 42.700 distance: 86 - 87: 55.322 distance: 86 - 89: 38.541 distance: 87 - 92: 20.965 distance: 88 - 116: 33.770 distance: 89 - 90: 38.854 distance: 89 - 91: 8.578 distance: 92 - 93: 23.476 distance: 93 - 94: 41.755 distance: 93 - 96: 29.769 distance: 94 - 103: 34.137 distance: 95 - 122: 31.108 distance: 96 - 97: 21.349 distance: 97 - 98: 30.774 distance: 98 - 99: 39.760 distance: 99 - 100: 60.384 distance: 100 - 101: 49.425 distance: 100 - 102: 54.434