Starting phenix.real_space_refine on Tue Mar 26 01:04:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugu_26406/03_2024/7ugu_26406.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugu_26406/03_2024/7ugu_26406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugu_26406/03_2024/7ugu_26406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugu_26406/03_2024/7ugu_26406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugu_26406/03_2024/7ugu_26406.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugu_26406/03_2024/7ugu_26406.pdb" } resolution = 2.6 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= 0.000 sd= 0.066 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 16728 2.51 5 N 4488 2.21 5 O 5272 1.98 5 H 26176 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 53": "OD1" <-> "OD2" Residue "G ASP 86": "OD1" <-> "OD2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "G TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G ASP 384": "OD1" <-> "OD2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 213": "OE1" <-> "OE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "H PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 281": "OE1" <-> "OE2" Residue "H GLU 353": "OE1" <-> "OE2" Residue "H GLU 378": "OE1" <-> "OE2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E ASP 320": "OD1" <-> "OD2" Residue "E ASP 384": "OD1" <-> "OD2" Residue "F ASP 14": "OD1" <-> "OD2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "F TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F GLU 213": "OE1" <-> "OE2" Residue "F PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 301": "OD1" <-> "OD2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "F GLU 378": "OE1" <-> "OE2" Residue "F ASP 384": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 320": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C ASP 416": "OD1" <-> "OD2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ASP 384": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52752 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 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: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 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: "E" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 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: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 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: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 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: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 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: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 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: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 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: 21.17, per 1000 atoms: 0.40 Number of scatterers: 52752 At special positions: 0 Unit cell: (174.22, 175.51, 80.012, 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 4488 7.00 C 16728 6.00 H 26176 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: 38.74 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: 156 helices and 32 sheets defined 48.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 64 through 74 Processing helix chain 'G' and resid 74 through 80 removed outlier: 3.602A 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: 3.727A pdb=" N VAL G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 136 Processing helix chain 'G' and resid 153 through 156 removed outlier: 3.652A 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 196 Processing helix chain 'G' and resid 214 through 230 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 286 Processing helix chain 'G' and resid 299 through 311 Processing helix chain 'G' and resid 325 through 335 Processing helix chain 'G' and resid 344 through 349 removed outlier: 4.045A pdb=" N ILE G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 364 removed outlier: 3.545A pdb=" N GLU G 356 " --> pdb=" O THR G 352 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA G 361 " --> pdb=" O ALA G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 389 removed outlier: 4.131A pdb=" N ASP G 384 " --> pdb=" O SER G 380 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL G 387 " --> pdb=" O ALA G 383 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR G 389 " --> pdb=" O ILE G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 419 removed outlier: 5.314A pdb=" N LYS G 407 " --> pdb=" O ASP G 403 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR G 408 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN G 410 " --> pdb=" O ALA G 406 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU G 411 " --> pdb=" O LYS G 407 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY G 419 " --> pdb=" O GLU G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 422 No H-bonds generated for 'chain 'G' and resid 420 through 422' Processing helix chain 'G' and resid 426 through 430 Processing helix chain 'H' and resid 58 through 62 Processing helix chain 'H' and resid 64 through 74 Processing helix chain 'H' and resid 74 through 80 removed outlier: 3.725A pdb=" N ALA H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 99 Processing helix chain 'H' and resid 107 through 127 removed outlier: 3.557A pdb=" N GLY H 113 " --> pdb=" O ASN H 109 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.516A 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 196 removed outlier: 3.590A pdb=" N ARG H 180 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS H 190 " --> pdb=" O PHE H 186 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS H 191 " --> pdb=" O HIS H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 229 Processing helix chain 'H' and resid 260 through 262 No H-bonds generated for 'chain 'H' and resid 260 through 262' Processing helix chain 'H' and resid 271 through 286 Processing helix chain 'H' and resid 299 through 311 removed outlier: 3.606A pdb=" N VAL H 305 " --> pdb=" O ASP H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 336 removed outlier: 3.704A pdb=" N ARG H 331 " --> pdb=" O GLU H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 349 removed outlier: 3.954A pdb=" N ILE H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 364 removed outlier: 3.566A pdb=" N ALA H 364 " --> pdb=" O MET H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 389 removed outlier: 4.175A pdb=" N ASP H 384 " --> pdb=" O SER H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 419 removed outlier: 5.690A pdb=" N LYS H 407 " --> pdb=" O ASP H 403 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY H 419 " --> pdb=" O GLU H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 422 No H-bonds generated for 'chain 'H' and resid 420 through 422' Processing helix chain 'H' and resid 426 through 430 Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 74 through 80 removed outlier: 3.616A 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: 3.754A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 120 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 153 through 156 removed outlier: 3.691A 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 196 Processing helix chain 'E' and resid 214 through 230 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 Processing helix chain 'E' and resid 299 through 311 Processing helix chain 'E' and resid 325 through 335 Processing helix chain 'E' and resid 344 through 349 removed outlier: 4.034A pdb=" N ILE E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 364 removed outlier: 3.535A pdb=" N GLU E 356 " --> pdb=" O THR E 352 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 389 removed outlier: 4.132A pdb=" N ASP E 384 " --> pdb=" O SER E 380 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR E 389 " --> pdb=" O ILE E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 419 removed outlier: 5.359A pdb=" N LYS E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 422 No H-bonds generated for 'chain 'E' and resid 420 through 422' Processing helix chain 'E' and resid 426 through 430 Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 64 through 74 Processing helix chain 'F' and resid 74 through 80 removed outlier: 3.749A pdb=" N ALA F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 99 Processing helix chain 'F' and resid 107 through 127 removed outlier: 3.541A pdb=" N ILE F 111 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY F 113 " --> pdb=" O ASN F 109 " (cutoff:3.500A) removed outlier: 3.515A 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 Processing helix chain 'F' and resid 174 through 197 removed outlier: 3.620A pdb=" N ARG F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS F 190 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS F 191 " --> pdb=" O HIS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 229 removed outlier: 3.584A pdb=" N GLY F 218 " --> pdb=" O GLY F 214 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL F 219 " --> pdb=" O THR F 215 " (cutoff:3.500A) 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 286 Processing helix chain 'F' and resid 299 through 311 Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.742A pdb=" N ARG F 331 " --> pdb=" O GLU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 349 removed outlier: 3.913A pdb=" N ILE F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 364 removed outlier: 3.500A pdb=" N THR F 354 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 364 " --> pdb=" O MET F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 4.119A pdb=" N ASP F 384 " --> pdb=" O SER F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 419 removed outlier: 5.684A pdb=" N LYS F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 422 No H-bonds generated for 'chain 'F' and resid 420 through 422' Processing helix chain 'F' and resid 426 through 430 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 64 through 74 Processing helix chain 'C' and resid 74 through 80 removed outlier: 3.667A 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: 3.728A pdb=" N VAL C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 120 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.628A 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 196 Processing helix chain 'C' and resid 214 through 230 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 Processing helix chain 'C' and resid 299 through 311 Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 344 through 349 removed outlier: 4.022A pdb=" N ILE C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 364 removed outlier: 3.515A pdb=" N GLU C 356 " --> pdb=" O THR C 352 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 removed outlier: 4.155A pdb=" N ASP C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C 389 " --> pdb=" O ILE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 419 removed outlier: 5.338A pdb=" N LYS C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 422 No H-bonds generated for 'chain 'C' and resid 420 through 422' Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 64 through 74 Processing helix chain 'D' and resid 74 through 80 removed outlier: 3.770A pdb=" N ALA D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 99 Processing helix chain 'D' and resid 107 through 127 removed outlier: 3.551A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 3.525A 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 Processing helix chain 'D' and resid 174 through 196 removed outlier: 3.603A pdb=" N ARG D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 229 removed outlier: 3.560A pdb=" N VAL D 219 " --> pdb=" O THR D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 271 through 286 Processing helix chain 'D' and resid 299 through 311 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.776A pdb=" N ARG D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 349 removed outlier: 3.970A pdb=" N ILE D 348 " --> pdb=" O LYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 364 removed outlier: 3.525A pdb=" N ALA D 364 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 389 removed outlier: 4.157A pdb=" N ASP D 384 " --> pdb=" O SER D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 419 removed outlier: 5.717A pdb=" N LYS D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 422 No H-bonds generated for 'chain 'D' and resid 420 through 422' Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.654A 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: 3.669A pdb=" N VAL A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.753A 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 196 Processing helix chain 'A' and resid 214 through 230 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 286 Processing helix chain 'A' and resid 299 through 311 Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 344 through 349 removed outlier: 4.000A pdb=" N ILE A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 364 removed outlier: 3.550A pdb=" N GLU A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 364 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 removed outlier: 4.075A pdb=" N ASP A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 419 removed outlier: 5.305A pdb=" N LYS A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 412 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.716A pdb=" N ALA B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'B' and resid 107 through 127 removed outlier: 3.534A pdb=" N ILE B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.546A 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 Processing helix chain 'B' and resid 174 through 196 removed outlier: 3.587A pdb=" N ARG B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 229 removed outlier: 3.685A pdb=" N VAL B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) 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 286 Processing helix chain 'B' and resid 299 through 311 Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.705A pdb=" N ARG B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 349 removed outlier: 3.959A pdb=" N ILE B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.519A pdb=" N THR B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 389 removed outlier: 4.169A pdb=" N ASP B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 419 removed outlier: 5.706A pdb=" N LYS B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 426 through 430 Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 13 removed outlier: 3.829A pdb=" N ASP G 6 " --> pdb=" O TYR G 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AA3, first strand: chain 'G' and resid 144 through 151 removed outlier: 7.001A pdb=" N PHE G 165 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE G 240 " --> pdb=" O ILE G 289 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE G 291 " --> pdb=" O ILE G 240 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE G 242 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE G 289 " --> pdb=" O GLN G 315 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL G 317 " --> pdb=" O ILE G 289 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE G 291 " --> pdb=" O VAL G 317 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU G 316 " --> pdb=" O SER G 340 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU G 342 " --> pdb=" O LEU G 316 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY G 318 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA G 368 " --> pdb=" O GLN G 393 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LYS G 395 " --> pdb=" O ALA G 368 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL G 370 " --> pdb=" O LYS G 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 250 through 251 removed outlier: 3.523A pdb=" N VAL G 256 " --> pdb=" O ASP G 251 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 13 removed outlier: 3.544A pdb=" N ASP H 6 " --> pdb=" O TYR H 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AA7, first strand: chain 'H' and resid 144 through 145 removed outlier: 6.435A pdb=" N THR H 144 " --> pdb=" O ILE H 394 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA H 368 " --> pdb=" O GLN H 393 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS H 395 " --> pdb=" O ALA H 368 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 370 " --> pdb=" O LYS H 395 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU H 316 " --> pdb=" O SER H 340 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU H 342 " --> pdb=" O LEU H 316 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY H 318 " --> pdb=" O LEU H 342 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE H 240 " --> pdb=" O THR H 290 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N GLU H 292 " --> pdb=" O ILE H 240 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE H 242 " --> pdb=" O GLU H 292 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE H 165 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 250 through 251 Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 13 removed outlier: 3.529A pdb=" N ASP E 6 " --> pdb=" O TYR E 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB2, first strand: chain 'E' and resid 144 through 151 removed outlier: 6.968A pdb=" N PHE E 165 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE E 240 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE E 291 " --> pdb=" O ILE E 240 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE E 242 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE E 289 " --> pdb=" O GLN E 315 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL E 317 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE E 291 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 316 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU E 342 " --> pdb=" O LEU E 316 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLY E 318 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA E 368 " --> pdb=" O GLN E 393 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LYS E 395 " --> pdb=" O ALA E 368 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL E 370 " --> pdb=" O LYS E 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 250 through 251 removed outlier: 3.550A pdb=" N VAL E 256 " --> pdb=" O ASP E 251 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 13 Processing sheet with id=AB5, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AB6, first strand: chain 'F' and resid 144 through 145 removed outlier: 6.415A pdb=" N THR F 144 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA F 368 " --> pdb=" O GLN F 393 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LYS F 395 " --> pdb=" O ALA F 368 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL F 370 " --> pdb=" O LYS F 395 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 316 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU F 342 " --> pdb=" O LEU F 316 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY F 318 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE F 240 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLU F 292 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE F 242 " --> pdb=" O GLU F 292 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE F 165 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 250 through 251 Processing sheet with id=AB8, first strand: chain 'C' and resid 4 through 13 removed outlier: 3.557A pdb=" N ASP C 6 " --> pdb=" O TYR C 26 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AC1, first strand: chain 'C' and resid 144 through 151 removed outlier: 6.916A pdb=" N PHE C 165 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE C 240 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 291 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE C 242 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE C 289 " --> pdb=" O GLN C 315 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL C 317 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 291 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 316 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU C 342 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY C 318 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA C 368 " --> pdb=" O GLN C 393 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS C 395 " --> pdb=" O ALA C 368 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL C 370 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.533A pdb=" N VAL C 256 " --> pdb=" O ASP C 251 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 13 removed outlier: 3.544A pdb=" N ASP D 6 " --> pdb=" O TYR D 26 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AC5, first strand: chain 'D' and resid 144 through 145 removed outlier: 6.410A pdb=" N THR D 144 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA D 368 " --> pdb=" O GLN D 393 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LYS D 395 " --> pdb=" O ALA D 368 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 370 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU D 316 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU D 342 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLY D 318 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE D 240 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N GLU D 292 " --> pdb=" O ILE D 240 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE D 242 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE D 165 " --> pdb=" O ILE D 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 250 through 251 Processing sheet with id=AC7, first strand: chain 'A' and resid 4 through 13 removed outlier: 3.763A pdb=" N ASP A 6 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 12 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AC9, first strand: chain 'A' and resid 144 through 151 removed outlier: 6.958A pdb=" N PHE A 165 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE A 240 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 291 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE A 242 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 289 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL A 317 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE A 291 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 316 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU A 342 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY A 318 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA A 368 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LYS A 395 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 370 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AD2, first strand: chain 'B' and resid 4 through 13 removed outlier: 6.981A pdb=" N TYR B 26 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL B 7 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU B 24 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA B 9 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU B 22 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU B 11 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B 20 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AD4, first strand: chain 'B' and resid 144 through 145 removed outlier: 6.492A pdb=" N THR B 144 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA B 368 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LYS B 395 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 370 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE B 240 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N GLU B 292 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE B 242 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE B 165 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 250 through 251 1240 hydrogen bonds defined for protein. 3513 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: 21.28 Time building geometry restraints manager: 40.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 5856 1.01 - 1.22: 20351 1.22 - 1.42: 11336 1.42 - 1.62: 15465 1.62 - 1.83: 168 Bond restraints: 53176 Sorted by residual: bond pdb=" N TYR F 259 " pdb=" H TYR F 259 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLY F 397 " pdb=" H GLY F 397 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N THR H 132 " pdb=" H THR H 132 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY F 349 " pdb=" H GLY F 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N TYR H 131 " pdb=" H TYR H 131 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 53171 not shown) Histogram of bond angle deviations from ideal: 94.67 - 102.74: 161 102.74 - 110.80: 52392 110.80 - 118.87: 22628 118.87 - 126.93: 20533 126.93 - 135.00: 374 Bond angle restraints: 96088 Sorted by residual: angle pdb=" O PHE B 137 " pdb=" C PHE B 137 " pdb=" N ASN B 138 " ideal model delta sigma weight residual 122.19 94.72 27.47 1.21e+00 6.83e-01 5.15e+02 angle pdb=" O PHE F 137 " pdb=" C PHE F 137 " pdb=" N ASN F 138 " ideal model delta sigma weight residual 122.19 94.85 27.34 1.21e+00 6.83e-01 5.11e+02 angle pdb=" O PHE G 137 " pdb=" C PHE G 137 " pdb=" N ASN G 138 " ideal model delta sigma weight residual 122.26 94.67 27.59 1.23e+00 6.61e-01 5.03e+02 angle pdb=" O PHE D 137 " pdb=" C PHE D 137 " pdb=" N ASN D 138 " ideal model delta sigma weight residual 122.19 95.08 27.11 1.21e+00 6.83e-01 5.02e+02 angle pdb=" O PHE C 137 " pdb=" C PHE C 137 " pdb=" N ASN C 138 " ideal model delta sigma weight residual 122.26 94.82 27.44 1.23e+00 6.61e-01 4.98e+02 ... (remaining 96083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 22612 17.89 - 35.78: 1443 35.78 - 53.68: 461 53.68 - 71.57: 296 71.57 - 89.46: 36 Dihedral angle restraints: 24848 sinusoidal: 13560 harmonic: 11288 Sorted by residual: dihedral pdb=" C THR F 396 " pdb=" N THR F 396 " pdb=" CA THR F 396 " pdb=" CB THR F 396 " ideal model delta harmonic sigma weight residual -122.00 -139.52 17.52 0 2.50e+00 1.60e-01 4.91e+01 dihedral pdb=" C THR H 396 " pdb=" N THR H 396 " pdb=" CA THR H 396 " pdb=" CB THR H 396 " ideal model delta harmonic sigma weight residual -122.00 -139.48 17.48 0 2.50e+00 1.60e-01 4.89e+01 dihedral pdb=" C THR D 396 " pdb=" N THR D 396 " pdb=" CA THR D 396 " pdb=" CB THR D 396 " ideal model delta harmonic sigma weight residual -122.00 -139.30 17.30 0 2.50e+00 1.60e-01 4.79e+01 ... (remaining 24845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3323 0.127 - 0.253: 688 0.253 - 0.380: 77 0.380 - 0.507: 12 0.507 - 0.634: 4 Chirality restraints: 4104 Sorted by residual: chirality pdb=" CA THR H 396 " pdb=" N THR H 396 " pdb=" C THR H 396 " pdb=" CB THR H 396 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA THR F 396 " pdb=" N THR F 396 " pdb=" C THR F 396 " pdb=" CB THR F 396 " both_signs ideal model delta sigma weight residual False 2.53 1.90 0.63 2.00e-01 2.50e+01 9.93e+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 1.90 0.63 2.00e-01 2.50e+01 9.80e+00 ... (remaining 4101 not shown) Planarity restraints: 8184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 404 " -0.020 9.50e-02 1.11e+02 1.86e-01 7.81e+02 pdb=" NE ARG D 404 " -0.109 2.00e-02 2.50e+03 pdb=" CZ ARG D 404 " -0.118 2.00e-02 2.50e+03 pdb=" NH1 ARG D 404 " -0.048 2.00e-02 2.50e+03 pdb=" NH2 ARG D 404 " -0.165 2.00e-02 2.50e+03 pdb="HH11 ARG D 404 " 0.136 2.00e-02 2.50e+03 pdb="HH12 ARG D 404 " 0.127 2.00e-02 2.50e+03 pdb="HH21 ARG D 404 " 0.410 2.00e-02 2.50e+03 pdb="HH22 ARG D 404 " -0.232 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 404 " -0.004 9.50e-02 1.11e+02 1.83e-01 7.53e+02 pdb=" NE ARG H 404 " 0.105 2.00e-02 2.50e+03 pdb=" CZ ARG H 404 " 0.115 2.00e-02 2.50e+03 pdb=" NH1 ARG H 404 " 0.048 2.00e-02 2.50e+03 pdb=" NH2 ARG H 404 " 0.167 2.00e-02 2.50e+03 pdb="HH11 ARG H 404 " -0.129 2.00e-02 2.50e+03 pdb="HH12 ARG H 404 " -0.130 2.00e-02 2.50e+03 pdb="HH21 ARG H 404 " -0.403 2.00e-02 2.50e+03 pdb="HH22 ARG H 404 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 404 " 0.027 9.50e-02 1.11e+02 1.83e-01 7.49e+02 pdb=" NE ARG F 404 " 0.106 2.00e-02 2.50e+03 pdb=" CZ ARG F 404 " 0.112 2.00e-02 2.50e+03 pdb=" NH1 ARG F 404 " 0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG F 404 " 0.165 2.00e-02 2.50e+03 pdb="HH11 ARG F 404 " -0.125 2.00e-02 2.50e+03 pdb="HH12 ARG F 404 " -0.126 2.00e-02 2.50e+03 pdb="HH21 ARG F 404 " -0.402 2.00e-02 2.50e+03 pdb="HH22 ARG F 404 " 0.232 2.00e-02 2.50e+03 ... (remaining 8181 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 2770 2.19 - 2.79: 88846 2.79 - 3.39: 142313 3.39 - 4.00: 193029 4.00 - 4.60: 284411 Nonbonded interactions: 711369 Sorted by model distance: nonbonded pdb=" HG SER E 247 " pdb=" OD1 ASP E 296 " model vdw 1.582 1.850 nonbonded pdb=" HG SER G 247 " pdb=" OD1 ASP G 296 " model vdw 1.583 1.850 nonbonded pdb=" HG1 THR B 5 " pdb=" OE2 GLU B 28 " model vdw 1.584 1.850 nonbonded pdb=" HG SER A 247 " pdb=" OD1 ASP A 296 " model vdw 1.590 1.850 nonbonded pdb=" HG SER C 247 " pdb=" OD1 ASP C 296 " model vdw 1.591 1.850 ... (remaining 711364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.770 Extract box with map and model: 6.440 Check model and map are aligned: 0.730 Set scattering table: 0.420 Process input model: 150.710 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.250 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:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.014 0.072 27000 Z= 0.905 Angle : 2.094 27.586 36512 Z= 1.429 Chirality : 0.104 0.634 4104 Planarity : 0.016 0.160 4792 Dihedral : 14.050 89.461 9880 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 0.73 % Allowed : 3.08 % Favored : 96.19 % Cbeta Deviations : 1.05 % 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: -2.11 (0.12), residues: 3472 helix: -1.30 (0.11), residues: 1512 sheet: 3.32 (0.43), residues: 80 loop : -1.69 (0.12), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.026 TRP G 303 HIS 0.017 0.005 HIS C 372 PHE 0.115 0.018 PHE H 137 TYR 0.181 0.025 TYR E 133 ARG 0.011 0.002 ARG G 404 *********************** 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 508 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 488 time to evaluate : 4.009 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: G 46 HIS cc_start: 0.6056 (m170) cc_final: 0.5817 (m170) REVERT: G 94 MET cc_start: 0.8490 (mtm) cc_final: 0.8025 (mtm) REVERT: G 231 TYR cc_start: 0.7537 (m-80) cc_final: 0.7228 (m-80) REVERT: G 295 MET cc_start: 0.8075 (mmt) cc_final: 0.6992 (mmt) REVERT: G 346 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7925 (p0) REVERT: G 404 ARG cc_start: 0.8261 (mpt180) cc_final: 0.8019 (mpt180) REVERT: H 1 MET cc_start: 0.7206 (mmp) cc_final: 0.6604 (mmp) REVERT: H 3 ILE cc_start: 0.7640 (mm) cc_final: 0.7404 (mp) REVERT: H 28 GLU cc_start: 0.6303 (tp30) cc_final: 0.6057 (mm-30) REVERT: H 53 ASP cc_start: 0.8150 (m-30) cc_final: 0.7858 (m-30) REVERT: E 94 MET cc_start: 0.8469 (mtm) cc_final: 0.7975 (mtm) REVERT: E 149 ILE cc_start: 0.8030 (pt) cc_final: 0.7700 (pt) REVERT: E 231 TYR cc_start: 0.7544 (m-80) cc_final: 0.7258 (m-80) REVERT: E 280 GLU cc_start: 0.6702 (tt0) cc_final: 0.6412 (tt0) REVERT: E 295 MET cc_start: 0.8193 (mmt) cc_final: 0.7643 (mmt) REVERT: E 346 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7981 (p0) REVERT: E 403 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8708 (p0) REVERT: E 404 ARG cc_start: 0.8215 (mpt180) cc_final: 0.7927 (mpt180) REVERT: F 3 ILE cc_start: 0.7631 (mm) cc_final: 0.7384 (OUTLIER) REVERT: F 53 ASP cc_start: 0.8170 (m-30) cc_final: 0.7826 (m-30) REVERT: F 85 ARG cc_start: 0.8087 (mtm180) cc_final: 0.7824 (mtm180) REVERT: C 46 HIS cc_start: 0.5656 (m-70) cc_final: 0.5435 (m-70) REVERT: C 58 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7846 (mtp180) REVERT: C 94 MET cc_start: 0.8476 (mtm) cc_final: 0.7990 (mtm) REVERT: C 295 MET cc_start: 0.8082 (mmt) cc_final: 0.7462 (mmt) REVERT: C 308 GLU cc_start: 0.6419 (tt0) cc_final: 0.6205 (tt0) REVERT: C 346 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7991 (p0) REVERT: D 3 ILE cc_start: 0.7634 (mm) cc_final: 0.7377 (mp) REVERT: D 79 ILE cc_start: 0.8383 (mm) cc_final: 0.8165 (mp) REVERT: D 186 PHE cc_start: 0.8014 (t80) cc_final: 0.7710 (t80) REVERT: D 334 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7360 (ttmt) REVERT: A 0 HIS cc_start: 0.7403 (m90) cc_final: 0.7109 (m170) REVERT: A 58 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7768 (mtp180) REVERT: A 94 MET cc_start: 0.8475 (mtm) cc_final: 0.7987 (mtm) REVERT: A 149 ILE cc_start: 0.7993 (pt) cc_final: 0.7666 (pt) REVERT: A 231 TYR cc_start: 0.7644 (m-80) cc_final: 0.7364 (m-80) REVERT: A 346 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7860 (p0) REVERT: A 403 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8811 (p0) REVERT: A 404 ARG cc_start: 0.8267 (mpt180) cc_final: 0.7962 (mpt180) REVERT: B 1 MET cc_start: 0.7070 (mmp) cc_final: 0.6683 (mmp) REVERT: B 3 ILE cc_start: 0.7636 (mm) cc_final: 0.7363 (mp) REVERT: B 79 ILE cc_start: 0.8367 (mm) cc_final: 0.8155 (mp) outliers start: 20 outliers final: 7 residues processed: 508 average time/residue: 3.0554 time to fit residues: 1798.0967 Evaluate side-chains 418 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 406 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 346 ASN Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 346 ASN Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 421 VAL 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: 0.9990 chunk 144 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 269 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS G 423 GLN H 423 GLN E 46 HIS C 0 HIS C 148 ASN A 423 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27000 Z= 0.240 Angle : 0.701 8.184 36512 Z= 0.404 Chirality : 0.044 0.190 4104 Planarity : 0.005 0.053 4792 Dihedral : 6.647 40.403 3805 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.13 % Allowed : 8.28 % Favored : 89.59 % 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: -1.14 (0.13), residues: 3472 helix: 0.48 (0.12), residues: 1480 sheet: -0.84 (0.27), residues: 280 loop : -1.91 (0.13), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 303 HIS 0.006 0.001 HIS A 372 PHE 0.022 0.002 PHE H 137 TYR 0.013 0.002 TYR G 131 ARG 0.004 0.001 ARG C 313 *********************** 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 504 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 446 time to evaluate : 3.468 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: G 94 MET cc_start: 0.8349 (mtm) cc_final: 0.7961 (mtm) REVERT: G 231 TYR cc_start: 0.7520 (m-80) cc_final: 0.7191 (m-80) REVERT: G 239 MET cc_start: 0.7085 (mtp) cc_final: 0.6832 (mtp) REVERT: G 295 MET cc_start: 0.7845 (mmt) cc_final: 0.6945 (mmt) REVERT: H 3 ILE cc_start: 0.7599 (mm) cc_final: 0.7344 (mp) REVERT: H 125 TYR cc_start: 0.7475 (t80) cc_final: 0.7216 (t80) REVERT: H 277 ASP cc_start: 0.5758 (m-30) cc_final: 0.5517 (m-30) REVERT: H 379 ASP cc_start: 0.6880 (t0) cc_final: 0.6619 (t0) REVERT: E 94 MET cc_start: 0.8328 (mtm) cc_final: 0.7954 (mtm) REVERT: E 231 TYR cc_start: 0.7590 (m-80) cc_final: 0.7244 (m-80) REVERT: E 239 MET cc_start: 0.7284 (mtp) cc_final: 0.7050 (mtp) REVERT: E 280 GLU cc_start: 0.6718 (tt0) cc_final: 0.6466 (tt0) REVERT: E 295 MET cc_start: 0.7907 (mmt) cc_final: 0.7354 (mmt) REVERT: E 362 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7595 (mmtt) REVERT: F 3 ILE cc_start: 0.7597 (mm) cc_final: 0.7309 (mp) REVERT: F 97 LEU cc_start: 0.7509 (tp) cc_final: 0.7141 (tp) REVERT: F 125 TYR cc_start: 0.7500 (t80) cc_final: 0.7260 (t80) REVERT: F 186 PHE cc_start: 0.7679 (t80) cc_final: 0.7172 (t80) REVERT: C 94 MET cc_start: 0.8349 (mtm) cc_final: 0.7960 (mtm) REVERT: C 239 MET cc_start: 0.7256 (mtp) cc_final: 0.6938 (mtp) REVERT: C 295 MET cc_start: 0.7880 (mmt) cc_final: 0.7002 (mmt) REVERT: C 410 GLN cc_start: 0.8341 (tp40) cc_final: 0.8133 (mm-40) REVERT: D 3 ILE cc_start: 0.7625 (mm) cc_final: 0.7331 (mp) REVERT: D 125 TYR cc_start: 0.7440 (t80) cc_final: 0.7200 (t80) REVERT: D 186 PHE cc_start: 0.7689 (t80) cc_final: 0.7442 (t80) REVERT: D 308 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6428 (tm-30) REVERT: A 0 HIS cc_start: 0.7326 (m90) cc_final: 0.7034 (m170) REVERT: A 94 MET cc_start: 0.8353 (mtm) cc_final: 0.7961 (mtm) REVERT: A 231 TYR cc_start: 0.7667 (m-80) cc_final: 0.7357 (m-80) REVERT: A 404 ARG cc_start: 0.8151 (mpt180) cc_final: 0.7918 (mpt180) REVERT: B 3 ILE cc_start: 0.7575 (mm) cc_final: 0.7282 (mp) REVERT: B 79 ILE cc_start: 0.8316 (mm) cc_final: 0.8115 (mp) REVERT: B 239 MET cc_start: 0.7890 (mtp) cc_final: 0.7646 (mtp) REVERT: B 379 ASP cc_start: 0.6948 (t0) cc_final: 0.6701 (t0) outliers start: 58 outliers final: 26 residues processed: 481 average time/residue: 2.5794 time to fit residues: 1472.7069 Evaluate side-chains 437 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 410 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 312 optimal weight: 1.9990 chunk 338 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS E 0 HIS E 46 HIS C 0 HIS A 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27000 Z= 0.273 Angle : 0.680 7.229 36512 Z= 0.389 Chirality : 0.045 0.178 4104 Planarity : 0.006 0.050 4792 Dihedral : 5.883 36.344 3788 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.93 % Allowed : 10.70 % Favored : 86.36 % 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: 0.65 (0.13), residues: 1480 sheet: -1.24 (0.22), residues: 432 loop : -2.02 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 303 HIS 0.005 0.001 HIS E 0 PHE 0.017 0.002 PHE H 137 TYR 0.016 0.002 TYR C 133 ARG 0.008 0.001 ARG E 313 *********************** 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 507 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 427 time to evaluate : 4.386 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: G 94 MET cc_start: 0.8397 (mtm) cc_final: 0.8005 (mtm) REVERT: G 231 TYR cc_start: 0.7466 (m-80) cc_final: 0.7249 (m-80) REVERT: G 239 MET cc_start: 0.7149 (mtp) cc_final: 0.6875 (mtp) REVERT: G 295 MET cc_start: 0.7873 (mmt) cc_final: 0.6967 (mmt) REVERT: H 3 ILE cc_start: 0.7626 (mm) cc_final: 0.7300 (mp) REVERT: H 28 GLU cc_start: 0.6338 (tp30) cc_final: 0.6107 (tp30) REVERT: H 47 GLU cc_start: 0.5853 (mt-10) cc_final: 0.5563 (mt-10) REVERT: H 190 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8059 (ttmp) REVERT: H 239 MET cc_start: 0.7956 (mtp) cc_final: 0.7486 (mtm) REVERT: H 334 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7431 (ttmt) REVERT: H 379 ASP cc_start: 0.7192 (t0) cc_final: 0.6843 (t0) REVERT: E 94 MET cc_start: 0.8381 (mtm) cc_final: 0.7992 (mtm) REVERT: E 98 ASP cc_start: 0.7486 (t0) cc_final: 0.7273 (t0) REVERT: E 231 TYR cc_start: 0.7598 (m-80) cc_final: 0.7328 (m-80) REVERT: E 239 MET cc_start: 0.7175 (mtp) cc_final: 0.6923 (mtp) REVERT: E 280 GLU cc_start: 0.6790 (tt0) cc_final: 0.6516 (tt0) REVERT: E 288 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7576 (mp) REVERT: F 3 ILE cc_start: 0.7694 (mm) cc_final: 0.7319 (mp) REVERT: F 47 GLU cc_start: 0.5813 (mt-10) cc_final: 0.5612 (mt-10) REVERT: F 97 LEU cc_start: 0.7731 (tp) cc_final: 0.7325 (tp) REVERT: F 239 MET cc_start: 0.7684 (mtp) cc_final: 0.7484 (mtm) REVERT: C 94 MET cc_start: 0.8404 (mtm) cc_final: 0.8013 (mtm) REVERT: C 204 ASP cc_start: 0.7775 (m-30) cc_final: 0.7462 (m-30) REVERT: C 239 MET cc_start: 0.7081 (mtp) cc_final: 0.6842 (mtp) REVERT: D 3 ILE cc_start: 0.7640 (mm) cc_final: 0.7239 (mp) REVERT: A 0 HIS cc_start: 0.7418 (m90) cc_final: 0.7102 (m170) REVERT: A 94 MET cc_start: 0.8380 (mtm) cc_final: 0.7969 (mtm) REVERT: A 166 MET cc_start: 0.7588 (mtm) cc_final: 0.7373 (mtm) REVERT: A 204 ASP cc_start: 0.7624 (m-30) cc_final: 0.7168 (m-30) REVERT: A 211 LYS cc_start: 0.7419 (mtmt) cc_final: 0.7109 (mttp) REVERT: A 288 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7695 (mp) REVERT: A 309 ARG cc_start: 0.6473 (tpp80) cc_final: 0.6251 (tpp80) REVERT: B 79 ILE cc_start: 0.8323 (mm) cc_final: 0.8075 (mp) REVERT: B 239 MET cc_start: 0.7932 (mtp) cc_final: 0.7464 (mtm) REVERT: B 253 GLU cc_start: 0.5789 (OUTLIER) cc_final: 0.5438 (mm-30) REVERT: B 379 ASP cc_start: 0.7089 (t0) cc_final: 0.6784 (t0) outliers start: 80 outliers final: 43 residues processed: 467 average time/residue: 2.5557 time to fit residues: 1429.3938 Evaluate side-chains 462 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 415 time to evaluate : 4.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 314 optimal weight: 0.0670 chunk 332 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 297 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 overall best weight: 2.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS G 423 GLN H 275 GLN E 0 HIS E 46 HIS E 423 GLN F 275 GLN C 0 HIS A 46 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27000 Z= 0.250 Angle : 0.631 6.395 36512 Z= 0.359 Chirality : 0.043 0.175 4104 Planarity : 0.005 0.050 4792 Dihedral : 5.638 36.227 3788 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.23 % Allowed : 11.91 % Favored : 84.86 % 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 (0.13), residues: 3472 helix: 0.85 (0.13), residues: 1480 sheet: -1.23 (0.22), residues: 432 loop : -2.13 (0.13), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 303 HIS 0.006 0.001 HIS A 372 PHE 0.015 0.002 PHE C 249 TYR 0.013 0.002 TYR C 133 ARG 0.004 0.001 ARG C 58 *********************** 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 509 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 421 time to evaluate : 3.669 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: G 94 MET cc_start: 0.8398 (mtm) cc_final: 0.8007 (mtm) REVERT: G 231 TYR cc_start: 0.7575 (m-80) cc_final: 0.7348 (m-80) REVERT: G 295 MET cc_start: 0.7908 (mmt) cc_final: 0.6948 (mmt) REVERT: H 3 ILE cc_start: 0.7621 (mm) cc_final: 0.7297 (mp) REVERT: H 47 GLU cc_start: 0.5972 (mt-10) cc_final: 0.5658 (mt-10) REVERT: H 190 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7945 (ttmp) REVERT: H 239 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7363 (mtm) REVERT: E 56 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6936 (mtpp) REVERT: E 94 MET cc_start: 0.8381 (mtm) cc_final: 0.7959 (mtm) REVERT: E 231 TYR cc_start: 0.7601 (m-80) cc_final: 0.7382 (m-80) REVERT: E 239 MET cc_start: 0.7088 (mtp) cc_final: 0.6877 (mtp) REVERT: E 280 GLU cc_start: 0.6800 (tt0) cc_final: 0.6565 (tt0) REVERT: E 288 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7582 (mp) REVERT: E 295 MET cc_start: 0.7853 (mmt) cc_final: 0.7512 (mmt) REVERT: E 362 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7541 (mmtt) REVERT: F 66 LYS cc_start: 0.7112 (mttt) cc_final: 0.6431 (mmmt) REVERT: F 97 LEU cc_start: 0.7744 (tp) cc_final: 0.7332 (tp) REVERT: C 56 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7017 (mtpp) REVERT: C 94 MET cc_start: 0.8405 (mtm) cc_final: 0.8009 (mtm) REVERT: C 239 MET cc_start: 0.7093 (mtp) cc_final: 0.6864 (mtp) REVERT: C 295 MET cc_start: 0.7820 (mmt) cc_final: 0.7049 (mmt) REVERT: D 3 ILE cc_start: 0.7685 (mm) cc_final: 0.7271 (mp) REVERT: D 281 GLU cc_start: 0.5713 (pt0) cc_final: 0.5405 (mt-10) REVERT: A 0 HIS cc_start: 0.7414 (m90) cc_final: 0.7112 (m170) REVERT: A 56 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6997 (mtpp) REVERT: A 94 MET cc_start: 0.8384 (mtm) cc_final: 0.7989 (mtm) REVERT: A 204 ASP cc_start: 0.7684 (m-30) cc_final: 0.7316 (m-30) REVERT: A 211 LYS cc_start: 0.7418 (mtmt) cc_final: 0.7058 (ttmm) REVERT: A 263 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.5979 (mp0) REVERT: A 288 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 363 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6205 (mm-30) REVERT: B 79 ILE cc_start: 0.8297 (mm) cc_final: 0.8041 (mp) REVERT: B 253 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5469 (mm-30) outliers start: 88 outliers final: 54 residues processed: 467 average time/residue: 2.3735 time to fit residues: 1321.6414 Evaluate side-chains 482 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 417 time to evaluate : 3.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 148 ASN Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 239 MET Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS H 275 GLN E 0 HIS E 46 HIS E 423 GLN F 275 GLN C 0 HIS C 423 GLN D 275 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 27000 Z= 0.316 Angle : 0.695 6.659 36512 Z= 0.394 Chirality : 0.045 0.180 4104 Planarity : 0.006 0.055 4792 Dihedral : 5.777 38.690 3788 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.03 % Allowed : 12.76 % Favored : 83.21 % 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: -1.36 (0.13), residues: 3472 helix: 0.55 (0.13), residues: 1480 sheet: -1.48 (0.24), residues: 376 loop : -2.19 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 303 HIS 0.006 0.001 HIS E 372 PHE 0.019 0.002 PHE E 249 TYR 0.017 0.002 TYR G 133 ARG 0.006 0.001 ARG H 373 *********************** 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 536 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 426 time to evaluate : 3.360 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: G 94 MET cc_start: 0.8372 (mtm) cc_final: 0.7956 (mtm) REVERT: G 140 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7291 (ptpp) REVERT: G 166 MET cc_start: 0.7795 (mtm) cc_final: 0.6559 (mmm) REVERT: G 231 TYR cc_start: 0.7627 (m-80) cc_final: 0.7378 (m-80) REVERT: G 280 GLU cc_start: 0.6884 (tt0) cc_final: 0.6684 (tt0) REVERT: G 295 MET cc_start: 0.7977 (mmt) cc_final: 0.6957 (mmt) REVERT: H 3 ILE cc_start: 0.7713 (mm) cc_final: 0.7329 (mp) REVERT: H 47 GLU cc_start: 0.6115 (mt-10) cc_final: 0.5669 (mt-10) REVERT: H 190 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7950 (ttmp) REVERT: H 239 MET cc_start: 0.8048 (mtp) cc_final: 0.7459 (mtm) REVERT: E 56 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6953 (mtpp) REVERT: E 94 MET cc_start: 0.8353 (mtm) cc_final: 0.7945 (mtm) REVERT: E 98 ASP cc_start: 0.7524 (t0) cc_final: 0.7322 (t0) REVERT: E 140 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7247 (ptpp) REVERT: E 231 TYR cc_start: 0.7640 (m-80) cc_final: 0.7395 (m-80) REVERT: E 280 GLU cc_start: 0.6802 (tt0) cc_final: 0.6539 (tt0) REVERT: E 288 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7689 (mp) REVERT: E 362 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7579 (mmtt) REVERT: F 47 GLU cc_start: 0.5855 (mt-10) cc_final: 0.5511 (mt-10) REVERT: C 56 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7002 (mtpp) REVERT: C 94 MET cc_start: 0.8381 (mtm) cc_final: 0.7962 (mtm) REVERT: C 140 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7291 (ptpp) REVERT: C 295 MET cc_start: 0.7850 (mmt) cc_final: 0.7144 (mmt) REVERT: D 3 ILE cc_start: 0.7675 (mm) cc_final: 0.7246 (mp) REVERT: D 281 GLU cc_start: 0.6060 (pt0) cc_final: 0.5817 (mt-10) REVERT: A 0 HIS cc_start: 0.7554 (m90) cc_final: 0.7255 (m170) REVERT: A 56 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6999 (mtpp) REVERT: A 94 MET cc_start: 0.8355 (mtm) cc_final: 0.7957 (mtm) REVERT: A 163 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: A 166 MET cc_start: 0.7607 (mtm) cc_final: 0.7326 (mtm) REVERT: A 211 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6926 (ttmm) REVERT: A 263 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6054 (mp0) REVERT: A 363 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6159 (mm-30) REVERT: B 79 ILE cc_start: 0.8266 (mm) cc_final: 0.8010 (mp) REVERT: B 253 GLU cc_start: 0.5813 (mm-30) cc_final: 0.5469 (mm-30) outliers start: 110 outliers final: 73 residues processed: 485 average time/residue: 2.2488 time to fit residues: 1304.0799 Evaluate side-chains 503 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 418 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 244 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 148 ASN Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 332 optimal weight: 0.5980 chunk 276 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS G 46 HIS H 275 GLN E 0 HIS E 46 HIS E 423 GLN F 275 GLN C 0 HIS C 148 ASN D 275 GLN A 46 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27000 Z= 0.270 Angle : 0.639 6.128 36512 Z= 0.362 Chirality : 0.043 0.173 4104 Planarity : 0.005 0.050 4792 Dihedral : 5.604 38.718 3788 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.33 % Allowed : 12.79 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3472 helix: 0.76 (0.13), residues: 1480 sheet: -1.66 (0.21), residues: 480 loop : -2.29 (0.13), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 303 HIS 0.008 0.001 HIS G 46 PHE 0.016 0.002 PHE E 249 TYR 0.014 0.002 TYR G 133 ARG 0.005 0.001 ARG C 58 *********************** 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 542 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 424 time to evaluate : 3.978 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: G 94 MET cc_start: 0.8387 (mtm) cc_final: 0.7957 (mtm) REVERT: G 140 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7316 (ptpp) REVERT: G 280 GLU cc_start: 0.6875 (tt0) cc_final: 0.6659 (tt0) REVERT: H 3 ILE cc_start: 0.7640 (mm) cc_final: 0.7322 (mp) REVERT: H 47 GLU cc_start: 0.6067 (mt-10) cc_final: 0.5625 (mt-10) REVERT: H 190 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7903 (ttmp) REVERT: H 239 MET cc_start: 0.7951 (mtp) cc_final: 0.7379 (mtm) REVERT: E 56 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6929 (mtpp) REVERT: E 94 MET cc_start: 0.8340 (mtm) cc_final: 0.7910 (mtm) REVERT: E 140 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7237 (ptpp) REVERT: E 166 MET cc_start: 0.7613 (mtm) cc_final: 0.7403 (mtm) REVERT: E 231 TYR cc_start: 0.7746 (m-80) cc_final: 0.7505 (m-80) REVERT: E 280 GLU cc_start: 0.6792 (tt0) cc_final: 0.6540 (tt0) REVERT: E 288 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7604 (mp) REVERT: E 295 MET cc_start: 0.7741 (mmt) cc_final: 0.7029 (mmt) REVERT: E 362 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7617 (mmtt) REVERT: F 47 GLU cc_start: 0.5998 (mt-10) cc_final: 0.5657 (mt-10) REVERT: F 194 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6844 (tptm) REVERT: C 56 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6985 (mtpp) REVERT: C 94 MET cc_start: 0.8365 (mtm) cc_final: 0.7957 (mtm) REVERT: C 140 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7257 (ptpp) REVERT: C 166 MET cc_start: 0.7659 (mtm) cc_final: 0.7344 (mtm) REVERT: C 363 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6526 (mm-30) REVERT: D 3 ILE cc_start: 0.7684 (mm) cc_final: 0.7253 (mp) REVERT: D 281 GLU cc_start: 0.6075 (pt0) cc_final: 0.5707 (mt-10) REVERT: D 312 LYS cc_start: 0.7939 (tppp) cc_final: 0.7439 (mppt) REVERT: A 0 HIS cc_start: 0.7547 (m90) cc_final: 0.7249 (m170) REVERT: A 56 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7005 (mtpp) REVERT: A 94 MET cc_start: 0.8333 (mtm) cc_final: 0.7914 (mtm) REVERT: A 166 MET cc_start: 0.7583 (mtm) cc_final: 0.7350 (mtm) REVERT: A 211 LYS cc_start: 0.7311 (mtmt) cc_final: 0.6946 (ttmm) REVERT: A 263 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6012 (mp0) REVERT: A 363 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5886 (mm-30) REVERT: B 79 ILE cc_start: 0.8256 (mm) cc_final: 0.7994 (mp) REVERT: B 105 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6655 (tppt) REVERT: B 194 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6718 (tptm) REVERT: B 253 GLU cc_start: 0.5685 (mm-30) cc_final: 0.5443 (mm-30) outliers start: 118 outliers final: 82 residues processed: 492 average time/residue: 2.1488 time to fit residues: 1268.0901 Evaluate side-chains 510 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 413 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 244 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 148 ASN Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS G 46 HIS H 275 GLN E 0 HIS E 46 HIS E 423 GLN F 275 GLN C 0 HIS D 275 GLN A 46 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27000 Z= 0.309 Angle : 0.680 7.035 36512 Z= 0.384 Chirality : 0.044 0.176 4104 Planarity : 0.006 0.050 4792 Dihedral : 5.684 39.838 3788 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.36 % Allowed : 13.05 % Favored : 82.59 % 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: -1.46 (0.13), residues: 3472 helix: 0.60 (0.13), residues: 1480 sheet: -1.69 (0.21), residues: 480 loop : -2.35 (0.13), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 303 HIS 0.009 0.001 HIS G 46 PHE 0.018 0.002 PHE E 249 TYR 0.016 0.002 TYR G 133 ARG 0.007 0.001 ARG D 373 *********************** 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 540 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 421 time to evaluate : 4.314 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: G 94 MET cc_start: 0.8375 (mtm) cc_final: 0.7992 (mtm) REVERT: G 140 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7324 (ptpp) REVERT: G 295 MET cc_start: 0.7833 (mmt) cc_final: 0.6927 (mmt) REVERT: H 3 ILE cc_start: 0.7645 (mm) cc_final: 0.7341 (mp) REVERT: H 47 GLU cc_start: 0.6140 (mt-10) cc_final: 0.5727 (mt-10) REVERT: H 190 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7922 (ttmp) REVERT: H 239 MET cc_start: 0.8002 (mtp) cc_final: 0.7442 (mtm) REVERT: E 56 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6765 (mtpp) REVERT: E 94 MET cc_start: 0.8335 (mtm) cc_final: 0.7927 (mtm) REVERT: E 140 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7275 (ptpp) REVERT: E 211 LYS cc_start: 0.7298 (mtmt) cc_final: 0.7085 (mtpm) REVERT: E 231 TYR cc_start: 0.7775 (m-80) cc_final: 0.7568 (m-80) REVERT: E 280 GLU cc_start: 0.6789 (tt0) cc_final: 0.6529 (tt0) REVERT: E 288 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7598 (mp) REVERT: E 295 MET cc_start: 0.7740 (mmt) cc_final: 0.7046 (mmt) REVERT: E 362 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7602 (mmtt) REVERT: F 47 GLU cc_start: 0.5994 (mt-10) cc_final: 0.5643 (mt-10) REVERT: F 194 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6868 (tptm) REVERT: C 56 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6868 (mtpp) REVERT: C 94 MET cc_start: 0.8404 (mtm) cc_final: 0.7970 (mtm) REVERT: C 140 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7317 (ptpp) REVERT: C 166 MET cc_start: 0.7674 (mtm) cc_final: 0.7329 (mtm) REVERT: D 3 ILE cc_start: 0.7573 (mm) cc_final: 0.7245 (mp) REVERT: D 281 GLU cc_start: 0.6081 (pt0) cc_final: 0.5699 (mt-10) REVERT: D 312 LYS cc_start: 0.7930 (tppp) cc_final: 0.7664 (tppt) REVERT: A 0 HIS cc_start: 0.7500 (m90) cc_final: 0.7209 (m170) REVERT: A 56 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7023 (mtpp) REVERT: A 94 MET cc_start: 0.8369 (mtm) cc_final: 0.7964 (mtm) REVERT: A 163 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: A 166 MET cc_start: 0.7578 (mtm) cc_final: 0.7358 (mtm) REVERT: A 211 LYS cc_start: 0.7342 (mtmt) cc_final: 0.6995 (ttmm) REVERT: A 263 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.5951 (mp0) REVERT: A 363 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5962 (mm-30) REVERT: B 79 ILE cc_start: 0.8283 (mm) cc_final: 0.8007 (mp) REVERT: B 164 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7133 (pt0) REVERT: B 194 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6742 (tptm) outliers start: 119 outliers final: 85 residues processed: 489 average time/residue: 1.9734 time to fit residues: 1154.0020 Evaluate side-chains 520 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 420 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 53 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 244 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 148 ASN Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 198 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS G 46 HIS H 275 GLN E 0 HIS E 46 HIS F 275 GLN C 0 HIS D 275 GLN A 46 HIS A 275 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27000 Z= 0.208 Angle : 0.578 5.753 36512 Z= 0.326 Chirality : 0.041 0.164 4104 Planarity : 0.005 0.047 4792 Dihedral : 5.339 37.965 3788 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.85 % Allowed : 13.89 % Favored : 82.26 % 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: -1.05 (0.14), residues: 3472 helix: 1.11 (0.13), residues: 1480 sheet: -1.56 (0.22), residues: 464 loop : -2.31 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 303 HIS 0.007 0.001 HIS G 46 PHE 0.012 0.002 PHE E 249 TYR 0.010 0.002 TYR E 59 ARG 0.004 0.000 ARG C 58 *********************** 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 539 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 434 time to evaluate : 2.859 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: G 94 MET cc_start: 0.8371 (mtm) cc_final: 0.7961 (mtm) REVERT: G 140 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7242 (ptpp) REVERT: G 295 MET cc_start: 0.7773 (mmt) cc_final: 0.6853 (mmt) REVERT: H 3 ILE cc_start: 0.7600 (mm) cc_final: 0.7267 (mp) REVERT: H 47 GLU cc_start: 0.5999 (mt-10) cc_final: 0.5548 (mt-10) REVERT: H 66 LYS cc_start: 0.7243 (mttt) cc_final: 0.6698 (mmmt) REVERT: H 105 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6441 (tppt) REVERT: H 190 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7928 (ttmp) REVERT: H 239 MET cc_start: 0.7933 (mtp) cc_final: 0.7509 (mtm) REVERT: E 56 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6767 (mtpp) REVERT: E 94 MET cc_start: 0.8314 (mtm) cc_final: 0.7902 (mtm) REVERT: E 140 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7253 (ptpp) REVERT: E 231 TYR cc_start: 0.7730 (m-80) cc_final: 0.7514 (m-80) REVERT: E 280 GLU cc_start: 0.6793 (tt0) cc_final: 0.6541 (tt0) REVERT: E 288 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7550 (mp) REVERT: E 295 MET cc_start: 0.7726 (mmt) cc_final: 0.7038 (mmt) REVERT: F 47 GLU cc_start: 0.5974 (mt-10) cc_final: 0.5610 (mt-10) REVERT: F 66 LYS cc_start: 0.7096 (mttt) cc_final: 0.6419 (mmmt) REVERT: F 194 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6837 (tptm) REVERT: C 56 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6865 (mtpp) REVERT: C 94 MET cc_start: 0.8349 (mtm) cc_final: 0.7964 (mtm) REVERT: C 140 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7232 (ptpp) REVERT: C 363 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6293 (mm-30) REVERT: D 281 GLU cc_start: 0.6076 (pt0) cc_final: 0.5696 (mt-10) REVERT: D 312 LYS cc_start: 0.7911 (tppp) cc_final: 0.7408 (mppt) REVERT: A 0 HIS cc_start: 0.7470 (m90) cc_final: 0.7193 (m170) REVERT: A 56 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7023 (mtpp) REVERT: A 94 MET cc_start: 0.8309 (mtm) cc_final: 0.7929 (mtm) REVERT: A 166 MET cc_start: 0.7642 (mtm) cc_final: 0.7338 (mtm) REVERT: A 211 LYS cc_start: 0.7315 (mtmt) cc_final: 0.6964 (ttmm) REVERT: A 363 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.5937 (mm-30) REVERT: B 79 ILE cc_start: 0.8270 (mm) cc_final: 0.8009 (mp) REVERT: B 164 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6994 (pt0) outliers start: 105 outliers final: 75 residues processed: 488 average time/residue: 1.8301 time to fit residues: 1072.9579 Evaluate side-chains 515 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 427 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 244 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 148 ASN Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 308 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 292 optimal weight: 0.7980 chunk 307 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS G 46 HIS G 148 ASN H 275 GLN E 0 HIS E 46 HIS F 275 GLN C 0 HIS D 275 GLN A 46 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27000 Z= 0.172 Angle : 0.538 6.207 36512 Z= 0.302 Chirality : 0.040 0.156 4104 Planarity : 0.004 0.045 4792 Dihedral : 5.061 36.072 3788 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.89 % Allowed : 14.04 % Favored : 82.07 % 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: -0.74 (0.14), residues: 3472 helix: 1.50 (0.14), residues: 1480 sheet: -1.48 (0.22), residues: 464 loop : -2.27 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 303 HIS 0.008 0.001 HIS G 46 PHE 0.010 0.001 PHE B 249 TYR 0.010 0.001 TYR F 26 ARG 0.003 0.000 ARG A 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 550 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 444 time to evaluate : 2.662 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: G 94 MET cc_start: 0.8391 (mtm) cc_final: 0.8006 (mtm) REVERT: G 140 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7293 (ptpp) REVERT: G 295 MET cc_start: 0.7756 (mmt) cc_final: 0.6843 (mmt) REVERT: H 3 ILE cc_start: 0.7668 (mm) cc_final: 0.7249 (mp) REVERT: H 47 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5522 (mt-10) REVERT: H 66 LYS cc_start: 0.7211 (mttt) cc_final: 0.6714 (mmmt) REVERT: H 105 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6400 (tppt) REVERT: H 190 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7866 (ttmp) REVERT: H 239 MET cc_start: 0.7837 (mtp) cc_final: 0.7384 (mtm) REVERT: H 334 LYS cc_start: 0.7653 (ttpt) cc_final: 0.7384 (ttmt) REVERT: E 56 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6756 (mtpp) REVERT: E 94 MET cc_start: 0.8352 (mtm) cc_final: 0.7943 (mtm) REVERT: E 140 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7320 (ptpp) REVERT: E 211 LYS cc_start: 0.7351 (mtpm) cc_final: 0.7133 (ttmm) REVERT: E 231 TYR cc_start: 0.7709 (m-80) cc_final: 0.7488 (m-80) REVERT: E 280 GLU cc_start: 0.6717 (tt0) cc_final: 0.6504 (tt0) REVERT: F 47 GLU cc_start: 0.5957 (mt-10) cc_final: 0.5562 (mt-10) REVERT: F 66 LYS cc_start: 0.7120 (mttt) cc_final: 0.6464 (mmmt) REVERT: F 194 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6846 (tttp) REVERT: C 56 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6857 (mtpp) REVERT: C 94 MET cc_start: 0.8382 (mtm) cc_final: 0.7985 (mtm) REVERT: C 140 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7300 (ptpp) REVERT: C 363 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6499 (mm-30) REVERT: D 281 GLU cc_start: 0.6076 (pt0) cc_final: 0.5690 (mt-10) REVERT: D 312 LYS cc_start: 0.7900 (tppp) cc_final: 0.7407 (mppt) REVERT: A 7 VAL cc_start: 0.8180 (p) cc_final: 0.7893 (p) REVERT: A 56 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7020 (mtpp) REVERT: A 94 MET cc_start: 0.8348 (mtm) cc_final: 0.7957 (mtm) REVERT: A 166 MET cc_start: 0.7619 (mtm) cc_final: 0.7312 (mtm) REVERT: A 211 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6958 (ttmm) REVERT: B 164 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6895 (pt0) outliers start: 106 outliers final: 73 residues processed: 496 average time/residue: 1.7169 time to fit residues: 1015.7231 Evaluate side-chains 514 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 430 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 244 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 148 ASN Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 0.7980 chunk 326 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 272 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 210 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS G 46 HIS H 275 GLN E 0 HIS E 46 HIS E 148 ASN F 275 GLN C 0 HIS D 275 GLN A 46 HIS A 148 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27000 Z= 0.212 Angle : 0.572 5.486 36512 Z= 0.322 Chirality : 0.041 0.162 4104 Planarity : 0.005 0.048 4792 Dihedral : 5.131 35.842 3788 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.81 % Allowed : 14.04 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3472 helix: 1.37 (0.14), residues: 1480 sheet: -1.48 (0.22), residues: 464 loop : -2.28 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 303 HIS 0.008 0.001 HIS G 46 PHE 0.013 0.002 PHE E 249 TYR 0.012 0.002 TYR G 133 ARG 0.003 0.000 ARG C 34 ********************** 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 538 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 434 time to evaluate : 2.785 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: G 94 MET cc_start: 0.8355 (mtm) cc_final: 0.7974 (mtm) REVERT: G 140 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7331 (ptpp) REVERT: G 166 MET cc_start: 0.7565 (mtm) cc_final: 0.6317 (mmm) REVERT: G 295 MET cc_start: 0.7759 (mmt) cc_final: 0.6856 (mmt) REVERT: H 3 ILE cc_start: 0.7714 (mm) cc_final: 0.7339 (mp) REVERT: H 47 GLU cc_start: 0.5953 (mt-10) cc_final: 0.5507 (mt-10) REVERT: H 66 LYS cc_start: 0.7263 (mttt) cc_final: 0.6734 (mmmt) REVERT: H 105 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6442 (tppt) REVERT: H 190 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7884 (ttmp) REVERT: H 239 MET cc_start: 0.7872 (mtp) cc_final: 0.7429 (mtm) REVERT: H 334 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7362 (ttmt) REVERT: E 56 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6775 (mtpp) REVERT: E 94 MET cc_start: 0.8315 (mtm) cc_final: 0.7924 (mtm) REVERT: E 140 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7332 (ptpp) REVERT: E 211 LYS cc_start: 0.7413 (mtpm) cc_final: 0.7175 (ttmm) REVERT: E 231 TYR cc_start: 0.7736 (m-80) cc_final: 0.7520 (m-80) REVERT: E 280 GLU cc_start: 0.6818 (tt0) cc_final: 0.6593 (tt0) REVERT: F 47 GLU cc_start: 0.5974 (mt-10) cc_final: 0.5608 (mt-10) REVERT: F 66 LYS cc_start: 0.7130 (mttt) cc_final: 0.6469 (mmmt) REVERT: F 164 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6909 (pt0) REVERT: F 194 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6898 (tttp) REVERT: C 56 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6880 (mtpp) REVERT: C 94 MET cc_start: 0.8343 (mtm) cc_final: 0.7934 (mtm) REVERT: C 140 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7307 (ptpp) REVERT: C 363 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6468 (mm-30) REVERT: D 3 ILE cc_start: 0.7666 (mm) cc_final: 0.7242 (mp) REVERT: D 164 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: D 281 GLU cc_start: 0.6091 (pt0) cc_final: 0.5701 (mt-10) REVERT: D 312 LYS cc_start: 0.7782 (tppp) cc_final: 0.7245 (mppt) REVERT: A 7 VAL cc_start: 0.8197 (p) cc_final: 0.7905 (p) REVERT: A 56 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7082 (mtpp) REVERT: A 94 MET cc_start: 0.8329 (mtm) cc_final: 0.7924 (mtm) REVERT: A 211 LYS cc_start: 0.7307 (mtmt) cc_final: 0.6961 (ttmm) REVERT: B 105 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6198 (tppt) REVERT: B 164 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6927 (pt0) outliers start: 104 outliers final: 75 residues processed: 490 average time/residue: 1.7361 time to fit residues: 1019.4107 Evaluate side-chains 518 residues out of total 2768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 429 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 36 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 215 THR Chi-restraints excluded: chain G residue 244 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 402 THR Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 148 ASN Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 211 LYS Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 317 VAL Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 244 CYS Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 312 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 301 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 280 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 0 HIS G 46 HIS H 275 GLN E 0 HIS E 46 HIS F 275 GLN C 0 HIS C 148 ASN D 275 GLN A 46 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.155094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135885 restraints weight = 75073.325| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.29 r_work: 0.3444 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27000 Z= 0.263 Angle : 0.623 6.246 36512 Z= 0.351 Chirality : 0.043 0.168 4104 Planarity : 0.005 0.050 4792 Dihedral : 5.340 36.750 3788 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.89 % Allowed : 14.11 % Favored : 82.00 % 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: -1.07 (0.14), residues: 3472 helix: 1.09 (0.13), residues: 1480 sheet: -1.54 (0.22), residues: 464 loop : -2.33 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 303 HIS 0.009 0.001 HIS G 46 PHE 0.016 0.002 PHE E 249 TYR 0.014 0.002 TYR C 133 ARG 0.005 0.001 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17463.22 seconds wall clock time: 302 minutes 39.25 seconds (18159.25 seconds total)