Starting phenix.real_space_refine on Tue Mar 26 00:22:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/03_2024/8dg4_27407.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/03_2024/8dg4_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_27407/03_2024/8dg4_27407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/03_2024/8dg4_27407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/03_2024/8dg4_27407.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg4_27407/03_2024/8dg4_27407.pdb" } resolution = 3.12 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= 0.001 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-dev-5265/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: 22.16, per 1000 atoms: 0.42 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: 39.51 Conformation dependent library (CDL) restraints added in 5.4 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: 4.91 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: 21.92 Time building geometry restraints manager: 41.18 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: 22485 17.05 - 34.10: 1346 34.10 - 51.15: 465 51.15 - 68.20: 381 68.20 - 85.25: 43 Dihedral angle restraints: 24720 sinusoidal: 13432 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 24717 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.730 Extract box with map and model: 6.300 Check model and map are aligned: 0.730 Set scattering table: 0.430 Process input model: 156.300 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.260 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.150 ------------------------------------------------------------------------------- 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 % Allowed : 3.23 % Favored : 96.62 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.022 TRP G 181 HIS 0.013 0.004 HIS B 372 PHE 0.059 0.011 PHE F 32 TYR 0.155 0.022 TYR A 259 ARG 0.012 0.002 ARG D 34 *********************** 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 : 3.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 MET cc_start: 0.8113 (mtm) cc_final: 0.7249 (mtm) REVERT: E 235 GLU cc_start: 0.7430 (pt0) cc_final: 0.7209 (pt0) REVERT: E 274 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: G 147 MET cc_start: 0.8202 (mtt) cc_final: 0.7884 (mtt) REVERT: G 295 MET cc_start: 0.8601 (mmm) cc_final: 0.8362 (mmm) REVERT: H 36 MET cc_start: 0.8163 (ptm) cc_final: 0.7921 (ptm) REVERT: H 243 ASP cc_start: 0.7399 (t0) cc_final: 0.7017 (t0) REVERT: C 94 MET cc_start: 0.7839 (mtm) cc_final: 0.7603 (mtm) REVERT: C 147 MET cc_start: 0.7702 (mtt) cc_final: 0.7483 (mtt) REVERT: C 295 MET cc_start: 0.8740 (mmm) cc_final: 0.8373 (mmm) REVERT: D 92 ARG cc_start: 0.7504 (mmt180) cc_final: 0.6918 (mmt90) REVERT: A 94 MET cc_start: 0.7966 (mtm) cc_final: 0.7447 (mtm) REVERT: A 147 MET cc_start: 0.8104 (mtt) cc_final: 0.7807 (mtt) REVERT: A 274 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: B 92 ARG cc_start: 0.7426 (mmt180) cc_final: 0.6959 (mmt90) REVERT: B 94 MET cc_start: 0.8665 (mtm) cc_final: 0.8309 (mtm) REVERT: B 348 ILE cc_start: 0.7556 (tp) cc_final: 0.7166 (tt) outliers start: 4 outliers final: 0 residues processed: 264 average time/residue: 0.9050 time to fit residues: 368.2198 Evaluate side-chains 183 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain A residue 274 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 269 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 312 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26872 Z= 0.194 Angle : 0.596 7.593 36384 Z= 0.337 Chirality : 0.042 0.166 4104 Planarity : 0.004 0.039 4792 Dihedral : 6.269 78.862 3790 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.67 % Allowed : 5.19 % Favored : 94.14 % 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: -1.13 (0.13), residues: 3472 helix: 0.16 (0.13), residues: 1536 sheet: -0.96 (0.23), residues: 408 loop : -1.60 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 181 HIS 0.005 0.001 HIS D 46 PHE 0.013 0.002 PHE E 321 TYR 0.015 0.001 TYR G 131 ARG 0.003 0.000 ARG D 58 *********************** 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 208 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 4.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 MET cc_start: 0.7861 (mtm) cc_final: 0.7107 (mtm) REVERT: E 213 GLU cc_start: 0.6597 (tm-30) cc_final: 0.6260 (tm-30) REVERT: F 359 GLU cc_start: 0.7097 (tt0) cc_final: 0.6824 (pt0) REVERT: G 147 MET cc_start: 0.7890 (mtt) cc_final: 0.7601 (mtt) REVERT: G 360 MET cc_start: 0.7686 (ttm) cc_final: 0.7486 (ttm) REVERT: H 359 GLU cc_start: 0.7272 (tt0) cc_final: 0.6965 (pt0) REVERT: C 213 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6490 (tm-30) REVERT: D 295 MET cc_start: 0.7783 (mmt) cc_final: 0.7578 (mmt) REVERT: D 319 ASP cc_start: 0.7702 (t0) cc_final: 0.7304 (t0) REVERT: A 94 MET cc_start: 0.7795 (mtm) cc_final: 0.7282 (mtm) REVERT: A 147 MET cc_start: 0.7865 (mtt) cc_final: 0.7537 (mtt) REVERT: A 213 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6671 (tm-30) REVERT: B 295 MET cc_start: 0.7520 (mmm) cc_final: 0.7266 (mmt) outliers start: 18 outliers final: 9 residues processed: 206 average time/residue: 0.9112 time to fit residues: 296.1807 Evaluate side-chains 170 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain B residue 403 ASP 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: 0.0060 chunk 338 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 106 optimal weight: 0.1980 chunk 251 optimal weight: 4.9990 overall best weight: 2.4402 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26872 Z= 0.268 Angle : 0.581 6.317 36384 Z= 0.327 Chirality : 0.043 0.164 4104 Planarity : 0.004 0.033 4792 Dihedral : 5.780 72.944 3784 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.85 % Allowed : 6.94 % Favored : 92.21 % 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: -1.27 (0.13), residues: 3472 helix: 0.41 (0.13), residues: 1480 sheet: -1.22 (0.23), residues: 424 loop : -1.98 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 303 HIS 0.004 0.002 HIS B 372 PHE 0.014 0.002 PHE C 186 TYR 0.019 0.002 TYR G 131 ARG 0.003 0.000 ARG G 401 *********************** 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 193 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 94 MET cc_start: 0.7733 (mtm) cc_final: 0.7084 (mtm) REVERT: E 213 GLU cc_start: 0.6630 (tm-30) cc_final: 0.6342 (tm-30) REVERT: E 403 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7631 (p0) REVERT: F 359 GLU cc_start: 0.7177 (tt0) cc_final: 0.6905 (pt0) REVERT: F 403 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7400 (p0) REVERT: G 94 MET cc_start: 0.7547 (mtm) cc_final: 0.6997 (mtm) REVERT: G 147 MET cc_start: 0.7963 (mtt) cc_final: 0.7614 (mtt) REVERT: H 168 MET cc_start: 0.7655 (mtp) cc_final: 0.7446 (mtp) REVERT: H 216 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6821 (tp30) REVERT: H 319 ASP cc_start: 0.7370 (t0) cc_final: 0.7124 (t0) REVERT: H 359 GLU cc_start: 0.7334 (tt0) cc_final: 0.6974 (pt0) REVERT: H 403 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7520 (p0) REVERT: C 213 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6764 (tm-30) REVERT: A 94 MET cc_start: 0.7666 (mtm) cc_final: 0.6922 (mtm) REVERT: A 146 MET cc_start: 0.8445 (ptp) cc_final: 0.7972 (mtm) REVERT: A 147 MET cc_start: 0.7953 (mtt) cc_final: 0.7485 (mtt) REVERT: B 166 MET cc_start: 0.7767 (mtt) cc_final: 0.7544 (mtt) REVERT: B 216 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: B 295 MET cc_start: 0.7645 (mmm) cc_final: 0.7247 (mmt) REVERT: B 319 ASP cc_start: 0.7353 (t0) cc_final: 0.7110 (t0) outliers start: 23 outliers final: 12 residues processed: 190 average time/residue: 0.9497 time to fit residues: 280.6623 Evaluate side-chains 172 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 4.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 299 ASP Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 403 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.7830 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26872 Z= 0.338 Angle : 0.608 6.125 36384 Z= 0.341 Chirality : 0.044 0.161 4104 Planarity : 0.005 0.038 4792 Dihedral : 5.837 73.748 3784 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.63 % Allowed : 7.79 % Favored : 90.58 % 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: -1.74 (0.13), residues: 3472 helix: 0.12 (0.13), residues: 1480 sheet: -1.32 (0.24), residues: 424 loop : -2.39 (0.12), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 303 HIS 0.006 0.002 HIS F 372 PHE 0.016 0.002 PHE H 186 TYR 0.020 0.002 TYR E 131 ARG 0.005 0.000 ARG A 401 *********************** 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 208 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 4.944 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: E 94 MET cc_start: 0.7627 (mtm) cc_final: 0.7053 (mtm) REVERT: E 213 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6506 (tm-30) REVERT: E 403 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7604 (p0) REVERT: F 359 GLU cc_start: 0.7170 (tt0) cc_final: 0.6918 (pt0) REVERT: G 147 MET cc_start: 0.8010 (mtt) cc_final: 0.7597 (mtt) REVERT: G 403 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7530 (p0) REVERT: H 295 MET cc_start: 0.8106 (mmt) cc_final: 0.7810 (mmt) REVERT: H 319 ASP cc_start: 0.7599 (t0) cc_final: 0.7319 (t0) REVERT: H 403 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7734 (p0) REVERT: C 94 MET cc_start: 0.7446 (mtm) cc_final: 0.7210 (mtm) REVERT: C 213 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6848 (tm-30) REVERT: C 403 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7565 (p0) REVERT: A 94 MET cc_start: 0.7602 (mtm) cc_final: 0.7005 (mtm) REVERT: A 146 MET cc_start: 0.8431 (ptp) cc_final: 0.7949 (mtm) REVERT: A 147 MET cc_start: 0.8043 (mtt) cc_final: 0.7602 (mtt) REVERT: A 403 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7628 (p0) REVERT: B 295 MET cc_start: 0.7556 (mmm) cc_final: 0.7173 (mmt) REVERT: B 319 ASP cc_start: 0.7537 (t0) cc_final: 0.7238 (t0) REVERT: B 403 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7921 (p0) outliers start: 44 outliers final: 23 residues processed: 204 average time/residue: 0.9945 time to fit residues: 313.2114 Evaluate side-chains 186 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain F residue 0 HIS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 299 ASP Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 403 ASP 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: 0.1980 chunk 137 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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: 0.7797 moved from start: 0.2889 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= 0.222 Angle : 0.521 5.300 36384 Z= 0.291 Chirality : 0.041 0.148 4104 Planarity : 0.004 0.043 4792 Dihedral : 5.493 70.849 3784 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.56 % Allowed : 8.64 % Favored : 89.80 % 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: -1.51 (0.13), residues: 3472 helix: 0.44 (0.13), residues: 1488 sheet: -1.17 (0.25), residues: 408 loop : -2.44 (0.12), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 303 HIS 0.003 0.001 HIS D 372 PHE 0.011 0.002 PHE F 249 TYR 0.014 0.002 TYR E 131 ARG 0.002 0.000 ARG G 313 *********************** 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 216 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 3.279 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: E 94 MET cc_start: 0.7595 (mtm) cc_final: 0.7181 (mtm) REVERT: E 213 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6394 (tm-30) REVERT: E 403 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7438 (p0) REVERT: F 359 GLU cc_start: 0.7156 (tt0) cc_final: 0.6904 (pt0) REVERT: G 147 MET cc_start: 0.7974 (mtt) cc_final: 0.7553 (mtt) REVERT: G 403 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7468 (p0) REVERT: H 295 MET cc_start: 0.8023 (mmt) cc_final: 0.7775 (mmt) REVERT: H 319 ASP cc_start: 0.7529 (t0) cc_final: 0.7328 (t0) REVERT: C 213 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6581 (tm-30) REVERT: A 94 MET cc_start: 0.7610 (mtm) cc_final: 0.7176 (mtm) REVERT: A 146 MET cc_start: 0.8350 (ptp) cc_final: 0.7932 (mtm) REVERT: A 147 MET cc_start: 0.8014 (mtt) cc_final: 0.7658 (mtt) REVERT: B 295 MET cc_start: 0.7471 (mmm) cc_final: 0.7005 (mmt) outliers start: 42 outliers final: 31 residues processed: 207 average time/residue: 0.9658 time to fit residues: 304.7528 Evaluate side-chains 196 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 299 ASP Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain D residue 0 HIS Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 403 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 332 optimal weight: 0.2980 chunk 276 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.7749 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26872 Z= 0.133 Angle : 0.454 4.531 36384 Z= 0.253 Chirality : 0.039 0.141 4104 Planarity : 0.003 0.043 4792 Dihedral : 5.020 66.849 3784 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.19 % Allowed : 9.53 % Favored : 89.28 % 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: -1.06 (0.14), residues: 3472 helix: 0.94 (0.14), residues: 1488 sheet: -1.03 (0.25), residues: 408 loop : -2.32 (0.12), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 300 HIS 0.002 0.001 HIS A 372 PHE 0.008 0.001 PHE F 249 TYR 0.009 0.001 TYR C 131 ARG 0.002 0.000 ARG A 313 *********************** 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 207 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 3.962 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: E 94 MET cc_start: 0.7578 (mtm) cc_final: 0.7290 (mtm) REVERT: E 213 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6253 (tm-30) REVERT: E 403 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7284 (p0) REVERT: F 359 GLU cc_start: 0.7100 (tt0) cc_final: 0.6881 (pt0) REVERT: G 94 MET cc_start: 0.7558 (mtm) cc_final: 0.6964 (mtm) REVERT: G 147 MET cc_start: 0.7974 (mtt) cc_final: 0.7542 (mtt) REVERT: G 403 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7338 (p0) REVERT: H 295 MET cc_start: 0.8012 (mmt) cc_final: 0.7741 (mmt) REVERT: C 213 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6424 (tm-30) REVERT: C 403 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7175 (p0) REVERT: A 94 MET cc_start: 0.7569 (mtm) cc_final: 0.7262 (mtm) REVERT: A 146 MET cc_start: 0.8316 (ptp) cc_final: 0.7911 (mtm) REVERT: A 147 MET cc_start: 0.7994 (mtt) cc_final: 0.7649 (mtt) REVERT: B 295 MET cc_start: 0.7473 (mmm) cc_final: 0.6911 (mmt) outliers start: 32 outliers final: 18 residues processed: 204 average time/residue: 0.9759 time to fit residues: 304.1914 Evaluate side-chains 184 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 299 ASP Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 403 ASP 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: 3.9990 chunk 189 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 280 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 331 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26872 Z= 0.205 Angle : 0.489 4.717 36384 Z= 0.272 Chirality : 0.041 0.144 4104 Planarity : 0.004 0.044 4792 Dihedral : 5.111 67.085 3784 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.37 % Allowed : 9.90 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3472 helix: 0.68 (0.14), residues: 1536 sheet: -0.99 (0.26), residues: 408 loop : -2.44 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 303 HIS 0.003 0.001 HIS A 46 PHE 0.012 0.001 PHE H 186 TYR 0.014 0.001 TYR A 131 ARG 0.002 0.000 ARG G 401 *********************** 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 204 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 MET cc_start: 0.7560 (mtm) cc_final: 0.7282 (mtm) REVERT: E 213 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6390 (tm-30) REVERT: F 359 GLU cc_start: 0.7168 (tt0) cc_final: 0.6947 (pt0) REVERT: G 94 MET cc_start: 0.7544 (mtm) cc_final: 0.6943 (mtm) REVERT: G 147 MET cc_start: 0.8015 (mtt) cc_final: 0.7581 (mtt) REVERT: G 403 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7377 (p0) REVERT: H 295 MET cc_start: 0.8035 (mmt) cc_final: 0.7780 (mmt) REVERT: C 213 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6470 (tm-30) REVERT: C 403 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7375 (p0) REVERT: A 94 MET cc_start: 0.7550 (mtm) cc_final: 0.7244 (mtm) REVERT: A 146 MET cc_start: 0.8326 (ptp) cc_final: 0.7925 (mtm) REVERT: A 147 MET cc_start: 0.8036 (mtt) cc_final: 0.7775 (mtt) REVERT: B 295 MET cc_start: 0.7399 (mmm) cc_final: 0.6827 (mmt) outliers start: 37 outliers final: 31 residues processed: 198 average time/residue: 0.9631 time to fit residues: 290.0549 Evaluate side-chains 197 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 299 ASP Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 403 ASP 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: 4.9990 chunk 198 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 210 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 163 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.7772 moved from start: 0.3180 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= 0.176 Angle : 0.472 4.636 36384 Z= 0.263 Chirality : 0.040 0.142 4104 Planarity : 0.003 0.044 4792 Dihedral : 5.026 66.438 3784 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.26 % Allowed : 10.13 % Favored : 88.61 % 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: -1.18 (0.14), residues: 3472 helix: 0.75 (0.14), residues: 1536 sheet: -0.97 (0.26), residues: 408 loop : -2.42 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.004 0.001 HIS H 46 PHE 0.010 0.001 PHE H 186 TYR 0.012 0.001 TYR A 131 ARG 0.002 0.000 ARG G 401 *********************** 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 200 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 MET cc_start: 0.7560 (mtm) cc_final: 0.7307 (mtm) REVERT: E 213 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6318 (tm-30) REVERT: F 359 GLU cc_start: 0.7150 (tt0) cc_final: 0.6943 (pt0) REVERT: G 94 MET cc_start: 0.7540 (mtm) cc_final: 0.6956 (mtm) REVERT: G 147 MET cc_start: 0.8001 (mtt) cc_final: 0.7589 (mtt) REVERT: H 295 MET cc_start: 0.7993 (mmt) cc_final: 0.7782 (mmt) REVERT: C 213 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6391 (tm-30) REVERT: C 403 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7315 (p0) REVERT: A 94 MET cc_start: 0.7541 (mtm) cc_final: 0.7259 (mtm) REVERT: A 146 MET cc_start: 0.8307 (ptp) cc_final: 0.7926 (mtm) REVERT: A 147 MET cc_start: 0.8031 (mtt) cc_final: 0.7805 (mtt) REVERT: B 295 MET cc_start: 0.7442 (mmm) cc_final: 0.6901 (mmt) outliers start: 34 outliers final: 29 residues processed: 197 average time/residue: 0.9610 time to fit residues: 286.9853 Evaluate side-chains 193 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 299 ASP Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 403 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 403 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 4.9990 chunk 317 optimal weight: 0.5980 chunk 289 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 0.0470 chunk 279 optimal weight: 0.9990 chunk 292 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- 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: 0.7732 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 26872 Z= 0.115 Angle : 0.428 4.424 36384 Z= 0.238 Chirality : 0.039 0.142 4104 Planarity : 0.003 0.044 4792 Dihedral : 4.693 62.160 3784 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.93 % Allowed : 10.57 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3472 helix: 1.10 (0.14), residues: 1536 sheet: -0.90 (0.26), residues: 408 loop : -2.27 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP H 300 HIS 0.002 0.001 HIS A 372 PHE 0.007 0.001 PHE E 32 TYR 0.008 0.001 TYR C 131 ARG 0.002 0.000 ARG D 58 *********************** 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 195 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 MET cc_start: 0.7627 (mtm) cc_final: 0.6994 (mtm) REVERT: E 213 GLU cc_start: 0.6431 (tm-30) cc_final: 0.6082 (tm-30) REVERT: F 359 GLU cc_start: 0.7132 (tt0) cc_final: 0.6877 (pt0) REVERT: G 94 MET cc_start: 0.7531 (mtm) cc_final: 0.6996 (mtm) REVERT: G 147 MET cc_start: 0.7988 (mtt) cc_final: 0.7569 (mtt) REVERT: H 295 MET cc_start: 0.7967 (mmt) cc_final: 0.7759 (mmt) REVERT: A 146 MET cc_start: 0.8219 (ptp) cc_final: 0.7845 (mtm) REVERT: B 295 MET cc_start: 0.7477 (mmm) cc_final: 0.6890 (mmt) outliers start: 25 outliers final: 23 residues processed: 194 average time/residue: 0.9861 time to fit residues: 292.0345 Evaluate side-chains 191 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 299 ASP Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 403 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 4.9990 chunk 326 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 227 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 315 optimal weight: 0.4980 chunk 272 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.7744 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 26872 Z= 0.143 Angle : 0.439 4.452 36384 Z= 0.244 Chirality : 0.039 0.139 4104 Planarity : 0.003 0.042 4792 Dihedral : 4.646 60.522 3784 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.15 % Allowed : 10.27 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3472 helix: 1.09 (0.14), residues: 1536 sheet: -0.83 (0.26), residues: 408 loop : -2.24 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 303 HIS 0.003 0.001 HIS H 46 PHE 0.010 0.001 PHE H 186 TYR 0.011 0.001 TYR C 131 ARG 0.001 0.000 ARG C 401 ********************** 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 198 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 4.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 MET cc_start: 0.7627 (mtm) cc_final: 0.6993 (mtm) REVERT: F 359 GLU cc_start: 0.7121 (tt0) cc_final: 0.6879 (pt0) REVERT: G 94 MET cc_start: 0.7530 (mtm) cc_final: 0.6989 (mtm) REVERT: G 147 MET cc_start: 0.8013 (mtt) cc_final: 0.7590 (mtt) REVERT: H 295 MET cc_start: 0.7982 (mmt) cc_final: 0.7773 (mmt) REVERT: A 146 MET cc_start: 0.8248 (ptp) cc_final: 0.7850 (mtm) REVERT: B 257 TYR cc_start: 0.7754 (m-80) cc_final: 0.7387 (m-80) REVERT: B 295 MET cc_start: 0.7470 (mmm) cc_final: 0.6898 (mmt) outliers start: 31 outliers final: 28 residues processed: 195 average time/residue: 1.0139 time to fit residues: 300.2580 Evaluate side-chains 191 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 389 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 313 ARG Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 299 ASP Chi-restraints excluded: chain H residue 403 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 403 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 280 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118489 restraints weight = 92044.743| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.80 r_work: 0.3318 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3314 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= 0.173 Angle : 0.462 4.519 36384 Z= 0.257 Chirality : 0.040 0.149 4104 Planarity : 0.003 0.042 4792 Dihedral : 4.759 62.104 3784 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.26 % Allowed : 10.50 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3472 helix: 0.97 (0.14), residues: 1536 sheet: -0.86 (0.26), residues: 408 loop : -2.30 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.003 0.001 HIS H 46 PHE 0.011 0.001 PHE H 186 TYR 0.012 0.001 TYR G 131 ARG 0.002 0.000 ARG C 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8782.46 seconds wall clock time: 156 minutes 22.34 seconds (9382.34 seconds total)