Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 20 17:05:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/07_2023/8dg4_27407.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/07_2023/8dg4_27407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/07_2023/8dg4_27407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/07_2023/8dg4_27407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/07_2023/8dg4_27407.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/07_2023/8dg4_27407.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.042 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: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 16632 2.51 5 N 4456 2.21 5 O 5272 1.98 5 H 25920 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 86": "OD1" <-> "OD2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 359": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 235": "OE1" <-> "OE2" Residue "F PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F GLU 308": "OE1" <-> "OE2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "G ASP 157": "OD1" <-> "OD2" Residue "G GLU 220": "OE1" <-> "OE2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 359": "OE1" <-> "OE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C GLU 220": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 274": "OE1" <-> "OE2" Residue "D GLU 327": "OE1" <-> "OE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ASP 379": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 52368 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6546 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6546 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6546 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6546 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6546 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6546 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6546 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6546 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 18.12, per 1000 atoms: 0.35 Number of scatterers: 52368 At special positions: 0 Unit cell: (176.73, 176.73, 77.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 O 5272 8.00 N 4456 7.00 C 16632 6.00 H 25920 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 37.09 Conformation dependent library (CDL) restraints added in 4.0 seconds 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6256 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 29 sheets defined 48.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.779A pdb=" N LEU E 60 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 74 through 80 removed outlier: 3.967A pdb=" N ALA E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 99 Processing helix chain 'E' and resid 107 through 126 removed outlier: 3.585A pdb=" N ALA E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 153 through 156 removed outlier: 3.569A pdb=" N SER E 156 " --> pdb=" O GLY E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 174 through 197 removed outlier: 3.645A pdb=" N ALA E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS E 191 " --> pdb=" O HIS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 230 removed outlier: 3.693A pdb=" N GLY E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 248 Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 271 through 286 removed outlier: 3.670A pdb=" N LYS E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 311 Processing helix chain 'E' and resid 325 through 336 removed outlier: 4.172A pdb=" N ARG E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 349 removed outlier: 4.046A pdb=" N ILE E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 364 Processing helix chain 'E' and resid 381 through 389 removed outlier: 3.955A pdb=" N VAL E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 418 removed outlier: 5.227A pdb=" N LYS E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 422 Processing helix chain 'E' and resid 425 through 430 removed outlier: 3.585A pdb=" N LYS E 428 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE E 430 " --> pdb=" O ILE E 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 64 through 74 removed outlier: 3.791A pdb=" N ASN F 70 " --> pdb=" O LYS F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 80 Processing helix chain 'F' and resid 86 through 99 Processing helix chain 'F' and resid 107 through 127 removed outlier: 3.587A pdb=" N ALA F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 153 through 156 removed outlier: 3.904A pdb=" N SER F 156 " --> pdb=" O GLY F 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 153 through 156' Processing helix chain 'F' and resid 174 through 197 removed outlier: 3.600A pdb=" N ARG F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY F 182 " --> pdb=" O GLY F 178 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS F 191 " --> pdb=" O HIS F 187 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 229 removed outlier: 3.596A pdb=" N ILE F 222 " --> pdb=" O GLY F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 248 Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 271 through 284 Processing helix chain 'F' and resid 299 through 311 Processing helix chain 'F' and resid 325 through 335 removed outlier: 4.338A pdb=" N ARG F 331 " --> pdb=" O GLU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 349 removed outlier: 3.968A pdb=" N ILE F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 363 removed outlier: 3.639A pdb=" N GLU F 356 " --> pdb=" O THR F 352 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 359 " --> pdb=" O PHE F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 4.255A pdb=" N ASP F 384 " --> pdb=" O SER F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 removed outlier: 5.293A pdb=" N LYS F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP F 416 " --> pdb=" O LEU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 422 removed outlier: 3.546A pdb=" N ALA F 422 " --> pdb=" O GLY F 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 419 through 422' Processing helix chain 'F' and resid 426 through 430 Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.748A pdb=" N LEU G 60 " --> pdb=" O SER G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 74 Processing helix chain 'G' and resid 74 through 80 removed outlier: 3.944A pdb=" N ALA G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 99 Processing helix chain 'G' and resid 107 through 126 removed outlier: 3.592A pdb=" N ALA G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 136 Processing helix chain 'G' and resid 153 through 156 removed outlier: 3.659A pdb=" N SER G 156 " --> pdb=" O GLY G 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 153 through 156' Processing helix chain 'G' and resid 174 through 197 removed outlier: 3.525A pdb=" N ARG G 180 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS G 191 " --> pdb=" O HIS G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 230 removed outlier: 3.651A pdb=" N GLY G 230 " --> pdb=" O ILE G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 248 Processing helix chain 'G' and resid 260 through 262 No H-bonds generated for 'chain 'G' and resid 260 through 262' Processing helix chain 'G' and resid 271 through 284 Processing helix chain 'G' and resid 299 through 311 Processing helix chain 'G' and resid 325 through 335 removed outlier: 4.141A pdb=" N ARG G 331 " --> pdb=" O GLU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 349 removed outlier: 4.055A pdb=" N ILE G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 364 Processing helix chain 'G' and resid 381 through 389 removed outlier: 4.025A pdb=" N VAL G 387 " --> pdb=" O ALA G 383 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR G 389 " --> pdb=" O ILE G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 418 removed outlier: 5.245A pdb=" N LYS G 407 " --> pdb=" O ASP G 403 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR G 408 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP G 416 " --> pdb=" O LEU G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 422 Processing helix chain 'G' and resid 426 through 430 removed outlier: 3.656A pdb=" N PHE G 430 " --> pdb=" O ILE G 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 62 Processing helix chain 'H' and resid 64 through 74 removed outlier: 3.711A pdb=" N ASN H 70 " --> pdb=" O LYS H 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 80 Processing helix chain 'H' and resid 86 through 99 Processing helix chain 'H' and resid 107 through 127 removed outlier: 3.559A pdb=" N ALA H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 136 Processing helix chain 'H' and resid 153 through 156 removed outlier: 3.871A pdb=" N SER H 156 " --> pdb=" O GLY H 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 153 through 156' Processing helix chain 'H' and resid 174 through 197 removed outlier: 3.551A pdb=" N ARG H 180 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY H 182 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS H 191 " --> pdb=" O HIS H 187 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 229 removed outlier: 3.631A pdb=" N ILE H 222 " --> pdb=" O GLY H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 248 Processing helix chain 'H' and resid 271 through 284 Processing helix chain 'H' and resid 299 through 311 Processing helix chain 'H' and resid 325 through 335 removed outlier: 4.286A pdb=" N ARG H 331 " --> pdb=" O GLU H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 349 removed outlier: 3.935A pdb=" N ILE H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 363 removed outlier: 3.655A pdb=" N GLU H 356 " --> pdb=" O THR H 352 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA H 357 " --> pdb=" O GLU H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 389 removed outlier: 4.245A pdb=" N ASP H 384 " --> pdb=" O SER H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 418 removed outlier: 5.321A pdb=" N LYS H 407 " --> pdb=" O ASP H 403 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP H 416 " --> pdb=" O LEU H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 422 removed outlier: 3.518A pdb=" N ALA H 422 " --> pdb=" O GLY H 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 419 through 422' Processing helix chain 'H' and resid 425 through 430 Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.741A pdb=" N LEU C 60 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 74 Processing helix chain 'C' and resid 74 through 80 removed outlier: 3.988A pdb=" N ALA C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 99 Processing helix chain 'C' and resid 107 through 126 removed outlier: 3.517A pdb=" N ILE C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.675A pdb=" N SER C 156 " --> pdb=" O GLY C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 174 through 197 removed outlier: 3.552A pdb=" N ARG C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 230 removed outlier: 3.677A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 248 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 271 through 286 removed outlier: 3.708A pdb=" N LYS C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 311 Processing helix chain 'C' and resid 325 through 335 removed outlier: 4.118A pdb=" N ARG C 331 " --> pdb=" O GLU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 349 removed outlier: 4.090A pdb=" N ILE C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 381 through 389 removed outlier: 4.027A pdb=" N VAL C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 418 removed outlier: 5.262A pdb=" N LYS C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 422 removed outlier: 3.555A pdb=" N ALA C 422 " --> pdb=" O GLY C 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 419 through 422' Processing helix chain 'C' and resid 426 through 430 removed outlier: 3.653A pdb=" N PHE C 430 " --> pdb=" O ILE C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.844A pdb=" N ASN D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 99 Processing helix chain 'D' and resid 107 through 127 removed outlier: 3.538A pdb=" N ALA D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 153 through 156 removed outlier: 3.786A pdb=" N SER D 156 " --> pdb=" O GLY D 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 153 through 156' Processing helix chain 'D' and resid 174 through 196 removed outlier: 3.515A pdb=" N ARG D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 229 removed outlier: 3.605A pdb=" N ILE D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 248 Processing helix chain 'D' and resid 271 through 284 Processing helix chain 'D' and resid 299 through 311 Processing helix chain 'D' and resid 325 through 335 removed outlier: 4.314A pdb=" N ARG D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 349 removed outlier: 3.955A pdb=" N ILE D 348 " --> pdb=" O LYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 removed outlier: 3.685A pdb=" N GLU D 356 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 359 " --> pdb=" O PHE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 389 removed outlier: 4.239A pdb=" N ASP D 384 " --> pdb=" O SER D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 418 removed outlier: 5.344A pdb=" N LYS D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 422 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.786A pdb=" N LEU A 60 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.955A pdb=" N ALA A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 107 through 126 removed outlier: 3.505A pdb=" N ILE A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.663A pdb=" N SER A 156 " --> pdb=" O GLY A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.514A pdb=" N ARG A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.672A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.058A pdb=" N ARG A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 4.094A pdb=" N ILE A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 381 through 389 removed outlier: 4.038A pdb=" N VAL A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 418 removed outlier: 5.233A pdb=" N LYS A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 422 removed outlier: 3.555A pdb=" N ALA A 422 " --> pdb=" O GLY A 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.670A pdb=" N PHE A 430 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 64 through 74 removed outlier: 3.812A pdb=" N ASN B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 107 through 127 removed outlier: 3.544A pdb=" N ALA B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 153 through 156 removed outlier: 3.857A pdb=" N SER B 156 " --> pdb=" O GLY B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 174 through 197 removed outlier: 3.561A pdb=" N ARG B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 229 removed outlier: 3.655A pdb=" N ILE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'B' and resid 299 through 311 Processing helix chain 'B' and resid 325 through 335 removed outlier: 4.350A pdb=" N ARG B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 349 removed outlier: 3.938A pdb=" N ILE B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.647A pdb=" N GLU B 356 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 389 removed outlier: 4.226A pdb=" N ASP B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 418 removed outlier: 5.312A pdb=" N LYS B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 422 removed outlier: 3.538A pdb=" N ALA B 422 " --> pdb=" O GLY B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 419 through 422' Processing helix chain 'B' and resid 425 through 430 Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 10 removed outlier: 3.611A pdb=" N ASP E 6 " --> pdb=" O TYR E 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 144 through 145 removed outlier: 6.335A pdb=" N THR E 144 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA E 368 " --> pdb=" O GLN E 393 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS E 395 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL E 370 " --> pdb=" O LYS E 395 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU E 316 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU E 342 " --> pdb=" O LEU E 316 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY E 318 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE E 289 " --> pdb=" O GLN E 315 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL E 317 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE E 291 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE E 240 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE E 291 " --> pdb=" O ILE E 240 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE E 242 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 164 " --> pdb=" O ASP E 243 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE E 165 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 250 through 251 Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 13 removed outlier: 3.801A pdb=" N ASP F 6 " --> pdb=" O TYR F 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'F' and resid 144 through 145 removed outlier: 6.365A pdb=" N THR F 144 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA F 368 " --> pdb=" O GLN F 393 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LYS F 395 " --> pdb=" O ALA F 368 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL F 370 " --> pdb=" O LYS F 395 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU F 316 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU F 342 " --> pdb=" O LEU F 316 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY F 318 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE F 289 " --> pdb=" O GLN F 315 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL F 317 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE F 291 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE F 240 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR F 290 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU F 292 " --> pdb=" O PHE F 242 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE F 150 " --> pdb=" O PHE F 165 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE F 167 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASN F 148 " --> pdb=" O ILE F 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 250 through 251 removed outlier: 3.504A pdb=" N VAL F 256 " --> pdb=" O ASP F 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 13 removed outlier: 3.608A pdb=" N ASP G 6 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL G 12 " --> pdb=" O THR G 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AB1, first strand: chain 'G' and resid 144 through 145 removed outlier: 6.370A pdb=" N THR G 144 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA G 368 " --> pdb=" O GLN G 393 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LYS G 395 " --> pdb=" O ALA G 368 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL G 370 " --> pdb=" O LYS G 395 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU G 316 " --> pdb=" O SER G 340 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU G 342 " --> pdb=" O LEU G 316 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY G 318 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE G 240 " --> pdb=" O ILE G 289 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE G 291 " --> pdb=" O ILE G 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE G 242 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU G 164 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE G 165 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 250 through 251 Processing sheet with id=AB3, first strand: chain 'H' and resid 4 through 13 removed outlier: 3.823A pdb=" N ASP H 6 " --> pdb=" O TYR H 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 144 through 145 removed outlier: 6.361A pdb=" N THR H 144 " --> pdb=" O ILE H 394 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA H 368 " --> pdb=" O GLN H 393 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LYS H 395 " --> pdb=" O ALA H 368 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL H 370 " --> pdb=" O LYS H 395 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU H 316 " --> pdb=" O SER H 340 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU H 342 " --> pdb=" O LEU H 316 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLY H 318 " --> pdb=" O LEU H 342 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE H 289 " --> pdb=" O GLN H 315 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL H 317 " --> pdb=" O ILE H 289 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE H 291 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE H 240 " --> pdb=" O ILE H 288 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR H 290 " --> pdb=" O ILE H 240 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU H 292 " --> pdb=" O PHE H 242 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE H 165 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 250 through 251 Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 13 removed outlier: 3.653A pdb=" N ASP C 6 " --> pdb=" O TYR C 26 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 12 " --> pdb=" O THR C 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB8, first strand: chain 'C' and resid 144 through 145 removed outlier: 6.342A pdb=" N THR C 144 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA C 368 " --> pdb=" O GLN C 393 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LYS C 395 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 370 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 316 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU C 342 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLY C 318 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE C 240 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 291 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE C 242 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU C 164 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE C 165 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 13 removed outlier: 3.812A pdb=" N ASP D 6 " --> pdb=" O TYR D 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AC3, first strand: chain 'D' and resid 144 through 145 removed outlier: 6.365A pdb=" N THR D 144 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ALA D 368 " --> pdb=" O GLN D 393 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LYS D 395 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL D 370 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU D 316 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU D 342 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY D 318 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE D 289 " --> pdb=" O GLN D 315 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL D 317 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 291 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE D 240 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR D 290 " --> pdb=" O ILE D 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 292 " --> pdb=" O PHE D 242 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 150 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE D 167 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASN D 148 " --> pdb=" O ILE D 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 250 through 251 Processing sheet with id=AC5, first strand: chain 'A' and resid 4 through 13 removed outlier: 3.578A pdb=" N ASP A 6 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 12 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AC7, first strand: chain 'A' and resid 144 through 151 removed outlier: 6.925A pdb=" N PHE A 165 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 164 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE A 240 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 291 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE A 242 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 316 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU A 342 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY A 318 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA A 368 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LYS A 395 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 370 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR A 144 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AC9, first strand: chain 'B' and resid 4 through 13 removed outlier: 3.869A pdb=" N ASP B 6 " --> pdb=" O TYR B 26 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 144 through 145 removed outlier: 6.355A pdb=" N THR B 144 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA B 368 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LYS B 395 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 370 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 316 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 342 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLY B 318 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE B 289 " --> pdb=" O GLN B 315 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL B 317 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 291 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE B 240 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 290 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 292 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 150 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 167 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASN B 148 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 250 through 251 1202 hydrogen bonds defined for protein. 3402 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: 21.54 Time building geometry restraints manager: 38.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.86: 1 0.86 - 1.10: 25911 1.10 - 1.34: 8453 1.34 - 1.58: 18259 1.58 - 1.82: 168 Bond restraints: 52792 Sorted by residual: bond pdb=" OG1 THR E 100 " pdb=" HG1 THR E 100 " ideal model delta sigma weight residual 0.840 0.616 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" CE2 PHE G 137 " pdb=" HE2 PHE G 137 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 PHE G 165 " pdb=" HE1 PHE G 165 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CZ2 TRP A 303 " pdb=" HZ2 TRP A 303 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASN A 70 " pdb=" H ASN A 70 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 52787 not shown) Histogram of bond angle deviations from ideal: 95.96 - 103.75: 308 103.75 - 111.53: 54993 111.53 - 119.32: 20959 119.32 - 127.10: 18826 127.10 - 134.89: 234 Bond angle restraints: 95320 Sorted by residual: angle pdb=" CA ASN E 109 " pdb=" CB ASN E 109 " pdb=" CG ASN E 109 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.39e+01 angle pdb=" CA ASN C 109 " pdb=" CB ASN C 109 " pdb=" CG ASN C 109 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA ASN G 109 " pdb=" CB ASN G 109 " pdb=" CG ASN G 109 " ideal model delta sigma weight residual 112.60 119.19 -6.59 1.00e+00 1.00e+00 4.34e+01 angle pdb=" CA ASN F 109 " pdb=" CB ASN F 109 " pdb=" CG ASN F 109 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 angle pdb=" CA ASN H 109 " pdb=" CB ASN H 109 " pdb=" CG ASN H 109 " ideal model delta sigma weight residual 112.60 118.79 -6.19 1.00e+00 1.00e+00 3.83e+01 ... (remaining 95315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 19321 17.05 - 34.10: 1019 34.10 - 51.15: 248 51.15 - 68.20: 225 68.20 - 85.25: 43 Dihedral angle restraints: 20856 sinusoidal: 9568 harmonic: 11288 Sorted by residual: dihedral pdb=" CA HIS G 46 " pdb=" C HIS G 46 " pdb=" N GLU G 47 " pdb=" CA GLU G 47 " ideal model delta harmonic sigma weight residual 180.00 151.02 28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA HIS A 46 " pdb=" C HIS A 46 " pdb=" N GLU A 47 " pdb=" CA GLU A 47 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA HIS C 46 " pdb=" C HIS C 46 " pdb=" N GLU C 47 " pdb=" CA GLU C 47 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 20853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2868 0.096 - 0.192: 1038 0.192 - 0.289: 156 0.289 - 0.385: 27 0.385 - 0.481: 15 Chirality restraints: 4104 Sorted by residual: chirality pdb=" CA THR E 402 " pdb=" N THR E 402 " pdb=" C THR E 402 " pdb=" CB THR E 402 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CA THR D 396 " pdb=" N THR D 396 " pdb=" C THR D 396 " pdb=" CB THR D 396 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ASN C 339 " pdb=" N ASN C 339 " pdb=" C ASN C 339 " pdb=" CB ASN C 339 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 4101 not shown) Planarity restraints: 8184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 404 " 0.206 9.50e-02 1.11e+02 1.26e-01 2.56e+02 pdb=" NE ARG G 404 " 0.083 2.00e-02 2.50e+03 pdb=" CZ ARG G 404 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG G 404 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG G 404 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG G 404 " -0.079 2.00e-02 2.50e+03 pdb="HH12 ARG G 404 " -0.079 2.00e-02 2.50e+03 pdb="HH21 ARG G 404 " -0.224 2.00e-02 2.50e+03 pdb="HH22 ARG G 404 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 404 " -0.202 9.50e-02 1.11e+02 1.22e-01 2.36e+02 pdb=" NE ARG E 404 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG E 404 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG E 404 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG E 404 " -0.055 2.00e-02 2.50e+03 pdb="HH11 ARG E 404 " 0.058 2.00e-02 2.50e+03 pdb="HH12 ARG E 404 " 0.092 2.00e-02 2.50e+03 pdb="HH21 ARG E 404 " 0.213 2.00e-02 2.50e+03 pdb="HH22 ARG E 404 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 404 " -0.163 9.50e-02 1.11e+02 1.13e-01 2.22e+02 pdb=" NE ARG C 404 " -0.071 2.00e-02 2.50e+03 pdb=" CZ ARG C 404 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG C 404 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG C 404 " -0.063 2.00e-02 2.50e+03 pdb="HH11 ARG C 404 " 0.062 2.00e-02 2.50e+03 pdb="HH12 ARG C 404 " 0.081 2.00e-02 2.50e+03 pdb="HH21 ARG C 404 " 0.212 2.00e-02 2.50e+03 pdb="HH22 ARG C 404 " -0.144 2.00e-02 2.50e+03 ... (remaining 8181 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2434 2.18 - 2.79: 89098 2.79 - 3.39: 138727 3.39 - 4.00: 187976 4.00 - 4.60: 279442 Nonbonded interactions: 697677 Sorted by model distance: nonbonded pdb=" OD1 ASP F 258 " pdb=" HG1 THR F 260 " model vdw 1.580 1.850 nonbonded pdb=" OD1 ASP B 258 " pdb=" HG1 THR B 260 " model vdw 1.585 1.850 nonbonded pdb=" OD1 ASP D 258 " pdb=" HG1 THR D 260 " model vdw 1.585 1.850 nonbonded pdb=" OD1 ASP H 258 " pdb=" HG1 THR H 260 " model vdw 1.589 1.850 nonbonded pdb=" OD2 ASP D 14 " pdb=" HG SER D 39 " model vdw 1.608 1.850 ... (remaining 697672 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' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.800 Extract box with map and model: 8.270 Check model and map are aligned: 0.610 Set scattering table: 0.360 Process input model: 144.590 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.013 0.045 26872 Z= 0.845 Angle : 1.929 8.218 36384 Z= 1.310 Chirality : 0.099 0.481 4104 Planarity : 0.012 0.090 4792 Dihedral : 13.651 85.251 9752 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 96.00 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.12), residues: 3472 helix: -1.75 (0.11), residues: 1520 sheet: 2.21 (0.40), residues: 168 loop : -1.37 (0.13), residues: 1784 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 261 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 264 average time/residue: 0.8702 time to fit residues: 353.2919 Evaluate side-chains 180 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 4.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 269 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 312 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 0 HIS H 0 HIS H 347 GLN D 0 HIS B 0 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 26872 Z= 0.196 Angle : 0.603 7.670 36384 Z= 0.341 Chirality : 0.042 0.168 4104 Planarity : 0.004 0.038 4792 Dihedral : 6.193 78.896 3784 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3472 helix: 0.14 (0.13), residues: 1536 sheet: -0.91 (0.23), residues: 408 loop : -1.55 (0.14), residues: 1528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 4.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 203 average time/residue: 0.8921 time to fit residues: 282.4734 Evaluate side-chains 167 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5627 time to fit residues: 13.5539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 338 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 347 GLN B 0 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 26872 Z= 0.386 Angle : 0.667 6.960 36384 Z= 0.375 Chirality : 0.046 0.174 4104 Planarity : 0.005 0.043 4792 Dihedral : 6.096 74.264 3784 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3472 helix: 0.00 (0.13), residues: 1480 sheet: -1.26 (0.23), residues: 424 loop : -2.17 (0.12), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 202 average time/residue: 0.8758 time to fit residues: 274.3312 Evaluate side-chains 171 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 4.034 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6875 time to fit residues: 16.6845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 332 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 284 ASN B 0 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 26872 Z= 0.291 Angle : 0.583 6.008 36384 Z= 0.326 Chirality : 0.043 0.157 4104 Planarity : 0.004 0.040 4792 Dihedral : 5.821 73.391 3784 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 3472 helix: 0.16 (0.13), residues: 1480 sheet: -1.32 (0.24), residues: 424 loop : -2.39 (0.12), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 183 average time/residue: 0.8828 time to fit residues: 249.5652 Evaluate side-chains 173 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 3.698 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.6160 time to fit residues: 18.4240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 0 HIS H 0 HIS B 0 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 26872 Z= 0.353 Angle : 0.618 6.006 36384 Z= 0.345 Chirality : 0.044 0.159 4104 Planarity : 0.005 0.047 4792 Dihedral : 5.898 72.184 3784 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3472 helix: -0.02 (0.13), residues: 1480 sheet: -1.33 (0.24), residues: 424 loop : -2.65 (0.12), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 188 average time/residue: 0.8987 time to fit residues: 257.9012 Evaluate side-chains 178 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 3.964 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6893 time to fit residues: 23.1133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 332 optimal weight: 0.6980 chunk 276 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 0 HIS B 0 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 26872 Z= 0.191 Angle : 0.509 5.071 36384 Z= 0.283 Chirality : 0.041 0.147 4104 Planarity : 0.004 0.046 4792 Dihedral : 5.464 70.019 3784 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 3472 helix: 0.47 (0.14), residues: 1488 sheet: -1.22 (0.25), residues: 408 loop : -2.59 (0.12), residues: 1576 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 185 average time/residue: 0.9182 time to fit residues: 258.4583 Evaluate side-chains 173 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 3.800 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4926 time to fit residues: 10.7088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 189 optimal weight: 2.9990 chunk 243 optimal weight: 0.3980 chunk 188 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 331 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 0 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 26872 Z= 0.145 Angle : 0.464 4.560 36384 Z= 0.257 Chirality : 0.040 0.140 4104 Planarity : 0.003 0.044 4792 Dihedral : 5.075 66.117 3784 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3472 helix: 0.88 (0.14), residues: 1488 sheet: -1.17 (0.25), residues: 408 loop : -2.46 (0.12), residues: 1576 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 180 average time/residue: 0.9400 time to fit residues: 256.5960 Evaluate side-chains 168 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 3.333 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4927 time to fit residues: 6.6482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 0 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 26872 Z= 0.299 Angle : 0.556 5.437 36384 Z= 0.309 Chirality : 0.043 0.148 4104 Planarity : 0.004 0.047 4792 Dihedral : 5.411 68.875 3784 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3472 helix: 0.33 (0.13), residues: 1536 sheet: -1.12 (0.25), residues: 408 loop : -2.68 (0.12), residues: 1528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 171 average time/residue: 0.9321 time to fit residues: 239.9571 Evaluate side-chains 170 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 3.173 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.8130 time to fit residues: 15.4679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 2.9990 chunk 317 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 279 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 0 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 26872 Z= 0.177 Angle : 0.485 4.739 36384 Z= 0.269 Chirality : 0.040 0.142 4104 Planarity : 0.003 0.045 4792 Dihedral : 5.176 67.419 3784 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3472 helix: 0.60 (0.14), residues: 1536 sheet: -1.13 (0.25), residues: 408 loop : -2.59 (0.13), residues: 1528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 178 average time/residue: 0.8893 time to fit residues: 240.0551 Evaluate side-chains 167 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 3.306 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5389 time to fit residues: 5.7082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 chunk 272 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 0 HIS B 0 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 26872 Z= 0.157 Angle : 0.463 4.528 36384 Z= 0.256 Chirality : 0.040 0.139 4104 Planarity : 0.003 0.040 4792 Dihedral : 4.917 64.449 3784 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3472 helix: 0.83 (0.14), residues: 1536 sheet: -1.07 (0.25), residues: 408 loop : -2.52 (0.13), residues: 1528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6944 Ramachandran restraints generated. 3472 Oldfield, 0 Emsley, 3472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 177 average time/residue: 0.9320 time to fit residues: 245.6146 Evaluate side-chains 172 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1177 time to fit residues: 6.8853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 280 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 0 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118221 restraints weight = 91929.044| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.84 r_work: 0.3320 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 26872 Z= 0.159 Angle : 0.462 4.509 36384 Z= 0.256 Chirality : 0.040 0.139 4104 Planarity : 0.003 0.038 4792 Dihedral : 4.864 63.598 3784 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3472 helix: 0.87 (0.14), residues: 1536 sheet: -1.05 (0.25), residues: 408 loop : -2.50 (0.13), residues: 1528 =============================================================================== Job complete usr+sys time: 7416.90 seconds wall clock time: 130 minutes 55.69 seconds (7855.69 seconds total)