Starting phenix.real_space_refine on Wed Feb 21 19:11:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8n_20688/02_2024/6u8n_20688_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8n_20688/02_2024/6u8n_20688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8n_20688/02_2024/6u8n_20688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8n_20688/02_2024/6u8n_20688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8n_20688/02_2024/6u8n_20688_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8n_20688/02_2024/6u8n_20688_updated.pdb" } resolution = 3.29 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= 0.073 sd= 2.647 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 P 72 5.49 5 S 176 5.16 5 C 19656 2.51 5 N 5400 2.21 5 O 6224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 407": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31528 Number of models: 1 Model: "" Number of chains: 24 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "B" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "C" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "D" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "E" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "F" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "G" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "H" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 16.39, per 1000 atoms: 0.52 Number of scatterers: 31528 At special positions: 0 Unit cell: (156.45, 156.45, 141.75, 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 176 16.00 P 72 15.00 O 6224 8.00 N 5400 7.00 C 19656 6.00 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.34 Conformation dependent library (CDL) restraints added in 6.6 seconds 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 48 sheets defined 32.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.57 Creating SS restraints... Processing helix chain 'I' and resid 2 through 5 No H-bonds generated for 'chain 'I' and resid 2 through 5' Processing helix chain 'A' and resid 20 through 26 removed outlier: 3.775A pdb=" N ASN A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.907A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.809A pdb=" N LYS A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.598A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 264 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 4.208A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.562A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'J' and resid 2 through 5 No H-bonds generated for 'chain 'J' and resid 2 through 5' Processing helix chain 'B' and resid 20 through 26 removed outlier: 3.776A pdb=" N ASN B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.907A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 109 removed outlier: 3.809A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.599A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 264 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 4.208A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.560A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'K' and resid 2 through 5 No H-bonds generated for 'chain 'K' and resid 2 through 5' Processing helix chain 'C' and resid 20 through 26 removed outlier: 3.776A pdb=" N ASN C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.906A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 109 removed outlier: 3.809A pdb=" N LYS C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 136 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.598A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 264 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 4.208A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.561A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'L' and resid 2 through 5 No H-bonds generated for 'chain 'L' and resid 2 through 5' Processing helix chain 'D' and resid 20 through 26 removed outlier: 3.776A pdb=" N ASN D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.907A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 109 removed outlier: 3.809A pdb=" N LYS D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.599A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 264 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 4.208A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.561A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'M' and resid 2 through 5 No H-bonds generated for 'chain 'M' and resid 2 through 5' Processing helix chain 'E' and resid 20 through 26 removed outlier: 3.776A pdb=" N ASN E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.907A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 109 removed outlier: 3.809A pdb=" N LYS E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 136 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.599A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA E 264 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 4.208A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 357 removed outlier: 3.561A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 417 through 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 500 Processing helix chain 'N' and resid 2 through 5 No H-bonds generated for 'chain 'N' and resid 2 through 5' Processing helix chain 'F' and resid 20 through 26 removed outlier: 3.775A pdb=" N ASN F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.907A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.810A pdb=" N LYS F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 225 through 227 No H-bonds generated for 'chain 'F' and resid 225 through 227' Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.598A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA F 264 " --> pdb=" O ASP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 4.208A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.561A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 457 through 471 Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 500 Processing helix chain 'O' and resid 2 through 5 No H-bonds generated for 'chain 'O' and resid 2 through 5' Processing helix chain 'G' and resid 20 through 26 removed outlier: 3.776A pdb=" N ASN G 25 " --> pdb=" O GLN G 21 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.907A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 109 removed outlier: 3.809A pdb=" N LYS G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 136 Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 225 through 227 No H-bonds generated for 'chain 'G' and resid 225 through 227' Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.599A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA G 264 " --> pdb=" O ASP G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 4.208A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 314 Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 357 removed outlier: 3.561A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 417 through 419 No H-bonds generated for 'chain 'G' and resid 417 through 419' Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 500 Processing helix chain 'P' and resid 2 through 5 No H-bonds generated for 'chain 'P' and resid 2 through 5' Processing helix chain 'H' and resid 20 through 26 removed outlier: 3.775A pdb=" N ASN H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.907A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 109 removed outlier: 3.809A pdb=" N LYS H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 136 Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.599A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 264 " --> pdb=" O ASP H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 4.208A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 314 Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 343 through 357 removed outlier: 3.561A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 417 through 419 No H-bonds generated for 'chain 'H' and resid 417 through 419' Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 500 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.708A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 320 through 323 removed outlier: 7.980A pdb=" N VAL A 323 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 362 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 383 " --> pdb=" O ALA A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 401 through 403 Processing sheet with id= E, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= F, first strand: chain 'A' and resid 208 through 212 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 247 through 249 removed outlier: 6.708A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 320 through 323 removed outlier: 7.980A pdb=" N VAL B 323 " --> pdb=" O PRO B 360 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 362 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B 383 " --> pdb=" O ALA B 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 401 through 403 Processing sheet with id= K, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= L, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 247 through 249 removed outlier: 6.708A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 320 through 323 removed outlier: 7.980A pdb=" N VAL C 323 " --> pdb=" O PRO C 360 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE C 362 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR C 383 " --> pdb=" O ALA C 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= Q, first strand: chain 'C' and resid 142 through 145 Processing sheet with id= R, first strand: chain 'C' and resid 208 through 212 Processing sheet with id= S, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'D' and resid 247 through 249 removed outlier: 6.708A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 320 through 323 removed outlier: 7.980A pdb=" N VAL D 323 " --> pdb=" O PRO D 360 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 362 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR D 383 " --> pdb=" O ALA D 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 401 through 403 Processing sheet with id= W, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= X, first strand: chain 'D' and resid 208 through 212 Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'E' and resid 247 through 249 removed outlier: 6.709A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 320 through 323 removed outlier: 7.980A pdb=" N VAL E 323 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE E 362 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 383 " --> pdb=" O ALA E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 401 through 403 Processing sheet with id= AC, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= AD, first strand: chain 'E' and resid 208 through 212 Processing sheet with id= AE, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'F' and resid 247 through 249 removed outlier: 6.708A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 320 through 323 removed outlier: 7.980A pdb=" N VAL F 323 " --> pdb=" O PRO F 360 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE F 362 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR F 383 " --> pdb=" O ALA F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 401 through 403 Processing sheet with id= AI, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AJ, first strand: chain 'F' and resid 208 through 212 Processing sheet with id= AK, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'G' and resid 247 through 249 removed outlier: 6.708A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'G' and resid 320 through 323 removed outlier: 7.980A pdb=" N VAL G 323 " --> pdb=" O PRO G 360 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE G 362 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR G 383 " --> pdb=" O ALA G 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'G' and resid 401 through 403 Processing sheet with id= AO, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AP, first strand: chain 'G' and resid 208 through 212 Processing sheet with id= AQ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'H' and resid 247 through 249 removed outlier: 6.709A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'H' and resid 320 through 323 removed outlier: 7.980A pdb=" N VAL H 323 " --> pdb=" O PRO H 360 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE H 362 " --> pdb=" O VAL H 323 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR H 383 " --> pdb=" O ALA H 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'H' and resid 401 through 403 Processing sheet with id= AU, first strand: chain 'H' and resid 142 through 145 Processing sheet with id= AV, first strand: chain 'H' and resid 208 through 212 744 hydrogen bonds defined for protein. 1992 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: 10.53 Time building geometry restraints manager: 14.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5285 1.30 - 1.42: 7683 1.42 - 1.55: 18572 1.55 - 1.68: 228 1.68 - 1.80: 304 Bond restraints: 32072 Sorted by residual: bond pdb=" C2' ATP E 601 " pdb=" C3' ATP E 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP D 601 " pdb=" C3' ATP D 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.82e+02 bond pdb=" C2' ATP F 601 " pdb=" C3' ATP F 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.81e+02 ... (remaining 32067 not shown) Histogram of bond angle deviations from ideal: 97.13 - 106.26: 1047 106.26 - 115.39: 19815 115.39 - 124.53: 21980 124.53 - 133.66: 582 133.66 - 142.79: 64 Bond angle restraints: 43488 Sorted by residual: angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 118.50 21.37 1.00e+00 1.00e+00 4.57e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 118.53 21.34 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 118.53 21.34 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 118.54 21.33 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 118.54 21.33 1.00e+00 1.00e+00 4.55e+02 ... (remaining 43483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 17016 16.34 - 32.69: 1712 32.69 - 49.03: 664 49.03 - 65.37: 432 65.37 - 81.72: 32 Dihedral angle restraints: 19856 sinusoidal: 8448 harmonic: 11408 Sorted by residual: dihedral pdb=" CA ILE F 437 " pdb=" C ILE F 437 " pdb=" N LYS F 438 " pdb=" CA LYS F 438 " ideal model delta harmonic sigma weight residual -180.00 -142.81 -37.19 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA ILE A 437 " pdb=" C ILE A 437 " pdb=" N LYS A 438 " pdb=" CA LYS A 438 " ideal model delta harmonic sigma weight residual -180.00 -142.81 -37.19 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA ILE E 437 " pdb=" C ILE E 437 " pdb=" N LYS E 438 " pdb=" CA LYS E 438 " ideal model delta harmonic sigma weight residual 180.00 -142.82 -37.18 0 5.00e+00 4.00e-02 5.53e+01 ... (remaining 19853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3032 0.064 - 0.127: 1404 0.127 - 0.191: 349 0.191 - 0.254: 142 0.254 - 0.318: 41 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CB VAL O 13 " pdb=" CA VAL O 13 " pdb=" CG1 VAL O 13 " pdb=" CG2 VAL O 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL M 13 " pdb=" CA VAL M 13 " pdb=" CG1 VAL M 13 " pdb=" CG2 VAL M 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL I 13 " pdb=" CA VAL I 13 " pdb=" CG1 VAL I 13 " pdb=" CG2 VAL I 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 4965 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 108 " -0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS H 108 " 0.070 2.00e-02 2.50e+03 pdb=" O LYS H 108 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS H 109 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 108 " 0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS F 108 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS F 108 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS F 109 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 108 " -0.021 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C LYS E 108 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS E 108 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS E 109 " -0.024 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8912 2.79 - 3.32: 30377 3.32 - 3.84: 54623 3.84 - 4.37: 63895 4.37 - 4.90: 103037 Nonbonded interactions: 260844 Sorted by model distance: nonbonded pdb=" O ALA B 83 " pdb=" OG SER B 237 " model vdw 2.260 2.440 nonbonded pdb=" O ALA G 83 " pdb=" OG SER G 237 " model vdw 2.260 2.440 nonbonded pdb=" O ALA A 83 " pdb=" OG SER A 237 " model vdw 2.260 2.440 nonbonded pdb=" O ALA E 83 " pdb=" OG SER E 237 " model vdw 2.260 2.440 nonbonded pdb=" O ALA H 83 " pdb=" OG SER H 237 " model vdw 2.260 2.440 ... (remaining 260839 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' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.490 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 83.840 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.019 0.290 32072 Z= 1.266 Angle : 1.891 21.373 43488 Z= 1.164 Chirality : 0.083 0.318 4968 Planarity : 0.007 0.044 5448 Dihedral : 17.956 81.715 12576 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.27 % Favored : 91.33 % Rotamer: Outliers : 9.05 % Allowed : 8.68 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.35 (0.11), residues: 3968 helix: -3.54 (0.09), residues: 1272 sheet: -2.60 (0.17), residues: 632 loop : -2.50 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 253 PHE 0.022 0.005 PHE A 131 TYR 0.033 0.004 TYR H 484 ARG 0.029 0.003 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1065 time to evaluate : 3.584 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: A 16 ASP cc_start: 0.8308 (t0) cc_final: 0.8050 (t0) REVERT: A 75 GLU cc_start: 0.6903 (pm20) cc_final: 0.6458 (pm20) REVERT: A 105 ARG cc_start: 0.8259 (mtm110) cc_final: 0.8023 (ttp80) REVERT: A 132 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: A 137 HIS cc_start: 0.8230 (m90) cc_final: 0.7973 (m-70) REVERT: A 157 ILE cc_start: 0.9101 (mm) cc_final: 0.8759 (mm) REVERT: A 179 MET cc_start: 0.7808 (pp-130) cc_final: 0.6937 (ppp) REVERT: A 198 ASN cc_start: 0.9205 (m-40) cc_final: 0.8666 (m-40) REVERT: A 209 LEU cc_start: 0.7847 (tt) cc_final: 0.7636 (tt) REVERT: A 214 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7963 (tm-30) REVERT: A 256 ASP cc_start: 0.8332 (p0) cc_final: 0.7620 (p0) REVERT: A 272 VAL cc_start: 0.8883 (t) cc_final: 0.8526 (m) REVERT: A 277 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8516 (tm-30) REVERT: A 319 ASP cc_start: 0.8203 (m-30) cc_final: 0.7771 (m-30) REVERT: A 327 SER cc_start: 0.8666 (p) cc_final: 0.8390 (p) REVERT: A 352 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 412 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7944 (ptt90) REVERT: A 496 SER cc_start: 0.9130 (p) cc_final: 0.8924 (p) REVERT: A 507 HIS cc_start: 0.8541 (t-90) cc_final: 0.7900 (t-90) REVERT: B 16 ASP cc_start: 0.8347 (t0) cc_final: 0.8142 (t0) REVERT: B 28 ASP cc_start: 0.8239 (m-30) cc_final: 0.8020 (m-30) REVERT: B 75 GLU cc_start: 0.6891 (pm20) cc_final: 0.6496 (pm20) REVERT: B 105 ARG cc_start: 0.8275 (mtm110) cc_final: 0.8050 (ttp80) REVERT: B 132 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8641 (pt0) REVERT: B 137 HIS cc_start: 0.8215 (m90) cc_final: 0.7961 (m-70) REVERT: B 157 ILE cc_start: 0.9145 (mm) cc_final: 0.8807 (mm) REVERT: B 179 MET cc_start: 0.7965 (pp-130) cc_final: 0.7109 (ppp) REVERT: B 198 ASN cc_start: 0.9110 (m-40) cc_final: 0.8563 (m-40) REVERT: B 199 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7810 (tp30) REVERT: B 203 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8177 (ttp-110) REVERT: B 206 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8284 (mtmm) REVERT: B 214 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8032 (tm-30) REVERT: B 256 ASP cc_start: 0.8383 (p0) cc_final: 0.7737 (p0) REVERT: B 277 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 319 ASP cc_start: 0.8227 (m-30) cc_final: 0.7976 (m-30) REVERT: B 327 SER cc_start: 0.8622 (p) cc_final: 0.8371 (p) REVERT: B 352 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 412 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8005 (ptt90) REVERT: B 470 ASP cc_start: 0.8947 (m-30) cc_final: 0.8720 (m-30) REVERT: B 496 SER cc_start: 0.9105 (p) cc_final: 0.8858 (p) REVERT: B 507 HIS cc_start: 0.8517 (t-90) cc_final: 0.7873 (t-90) REVERT: C 16 ASP cc_start: 0.8297 (t0) cc_final: 0.8051 (t0) REVERT: C 75 GLU cc_start: 0.6894 (pm20) cc_final: 0.6467 (pm20) REVERT: C 105 ARG cc_start: 0.8307 (mtm110) cc_final: 0.8070 (ttp80) REVERT: C 132 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8679 (pt0) REVERT: C 157 ILE cc_start: 0.9093 (mm) cc_final: 0.8784 (mm) REVERT: C 179 MET cc_start: 0.7783 (pp-130) cc_final: 0.7016 (ppp) REVERT: C 198 ASN cc_start: 0.9136 (m-40) cc_final: 0.8581 (m-40) REVERT: C 203 ARG cc_start: 0.8698 (tpp-160) cc_final: 0.8207 (ttp-110) REVERT: C 209 LEU cc_start: 0.7805 (tt) cc_final: 0.7596 (tt) REVERT: C 214 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7955 (tm-30) REVERT: C 256 ASP cc_start: 0.8384 (p0) cc_final: 0.7744 (p0) REVERT: C 277 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8467 (tm-30) REVERT: C 300 ILE cc_start: 0.8455 (mm) cc_final: 0.8238 (mm) REVERT: C 319 ASP cc_start: 0.8296 (m-30) cc_final: 0.7852 (m-30) REVERT: C 327 SER cc_start: 0.8612 (p) cc_final: 0.8334 (p) REVERT: C 352 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 412 ARG cc_start: 0.8426 (ttp80) cc_final: 0.7985 (ptt90) REVERT: C 496 SER cc_start: 0.9078 (p) cc_final: 0.8842 (p) REVERT: C 507 HIS cc_start: 0.8539 (t-90) cc_final: 0.7883 (t-90) REVERT: D 16 ASP cc_start: 0.8277 (t0) cc_final: 0.8013 (t0) REVERT: D 34 ASP cc_start: 0.9071 (t0) cc_final: 0.8821 (t0) REVERT: D 75 GLU cc_start: 0.7034 (pm20) cc_final: 0.6644 (pm20) REVERT: D 105 ARG cc_start: 0.8312 (mtm110) cc_final: 0.8055 (ttp80) REVERT: D 121 LEU cc_start: 0.8348 (mm) cc_final: 0.8147 (mp) REVERT: D 132 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: D 137 HIS cc_start: 0.8221 (m90) cc_final: 0.7973 (m-70) REVERT: D 157 ILE cc_start: 0.9145 (mm) cc_final: 0.8805 (mm) REVERT: D 179 MET cc_start: 0.7989 (pp-130) cc_final: 0.7109 (ppp) REVERT: D 198 ASN cc_start: 0.9186 (m-40) cc_final: 0.8624 (m-40) REVERT: D 214 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7980 (tm-30) REVERT: D 277 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8443 (tm-30) REVERT: D 286 MET cc_start: 0.8991 (tmt) cc_final: 0.8502 (tmt) REVERT: D 319 ASP cc_start: 0.8204 (m-30) cc_final: 0.7958 (m-30) REVERT: D 327 SER cc_start: 0.8646 (p) cc_final: 0.8403 (p) REVERT: D 352 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8373 (tm-30) REVERT: D 412 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8006 (ptt90) REVERT: D 470 ASP cc_start: 0.8881 (m-30) cc_final: 0.8678 (m-30) REVERT: D 507 HIS cc_start: 0.8567 (t-90) cc_final: 0.7914 (t-90) REVERT: E 26 CYS cc_start: 0.8516 (m) cc_final: 0.8315 (t) REVERT: E 34 ASP cc_start: 0.9042 (t0) cc_final: 0.8836 (t0) REVERT: E 75 GLU cc_start: 0.6940 (pm20) cc_final: 0.6515 (pm20) REVERT: E 105 ARG cc_start: 0.8244 (mtm110) cc_final: 0.8030 (ttp80) REVERT: E 132 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: E 137 HIS cc_start: 0.8304 (m90) cc_final: 0.8078 (m-70) REVERT: E 157 ILE cc_start: 0.9089 (mm) cc_final: 0.8803 (mm) REVERT: E 179 MET cc_start: 0.7828 (pp-130) cc_final: 0.7096 (ppp) REVERT: E 198 ASN cc_start: 0.9123 (m-40) cc_final: 0.8624 (m-40) REVERT: E 203 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8204 (ttp-110) REVERT: E 214 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7999 (tm-30) REVERT: E 256 ASP cc_start: 0.8280 (p0) cc_final: 0.7572 (p0) REVERT: E 272 VAL cc_start: 0.8852 (t) cc_final: 0.8572 (m) REVERT: E 277 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8463 (tm-30) REVERT: E 300 ILE cc_start: 0.8448 (mm) cc_final: 0.8235 (mm) REVERT: E 319 ASP cc_start: 0.8241 (m-30) cc_final: 0.7808 (m-30) REVERT: E 327 SER cc_start: 0.8587 (p) cc_final: 0.8319 (p) REVERT: E 352 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8351 (tm-30) REVERT: E 412 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8014 (ptt90) REVERT: E 496 SER cc_start: 0.9038 (p) cc_final: 0.8782 (p) REVERT: E 507 HIS cc_start: 0.8549 (t-90) cc_final: 0.7919 (t-90) REVERT: F 16 ASP cc_start: 0.8245 (t0) cc_final: 0.8023 (t0) REVERT: F 28 ASP cc_start: 0.8305 (m-30) cc_final: 0.8079 (m-30) REVERT: F 75 GLU cc_start: 0.7023 (pm20) cc_final: 0.6650 (pm20) REVERT: F 105 ARG cc_start: 0.8311 (mtm110) cc_final: 0.8019 (ttp80) REVERT: F 121 LEU cc_start: 0.8335 (mm) cc_final: 0.8131 (mp) REVERT: F 132 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: F 137 HIS cc_start: 0.8261 (m90) cc_final: 0.7997 (m-70) REVERT: F 157 ILE cc_start: 0.9143 (mm) cc_final: 0.8805 (mm) REVERT: F 179 MET cc_start: 0.7935 (pp-130) cc_final: 0.7053 (ppp) REVERT: F 198 ASN cc_start: 0.9145 (m-40) cc_final: 0.8696 (m-40) REVERT: F 199 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: F 203 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.8086 (ttp-170) REVERT: F 209 LEU cc_start: 0.7876 (tt) cc_final: 0.7671 (tt) REVERT: F 214 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7909 (tm-30) REVERT: F 277 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8412 (tm-30) REVERT: F 286 MET cc_start: 0.8992 (tmt) cc_final: 0.8527 (tmt) REVERT: F 319 ASP cc_start: 0.8222 (m-30) cc_final: 0.7836 (m-30) REVERT: F 327 SER cc_start: 0.8665 (p) cc_final: 0.8428 (p) REVERT: F 352 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8397 (tm-30) REVERT: F 412 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8008 (ptt90) REVERT: F 470 ASP cc_start: 0.8901 (m-30) cc_final: 0.8701 (m-30) REVERT: F 496 SER cc_start: 0.9005 (p) cc_final: 0.8788 (p) REVERT: F 507 HIS cc_start: 0.8560 (t-90) cc_final: 0.7933 (t-90) REVERT: G 16 ASP cc_start: 0.8301 (t0) cc_final: 0.8086 (t0) REVERT: G 34 ASP cc_start: 0.9063 (t0) cc_final: 0.8851 (t0) REVERT: G 75 GLU cc_start: 0.6973 (pm20) cc_final: 0.6562 (pm20) REVERT: G 105 ARG cc_start: 0.8287 (mtm110) cc_final: 0.8008 (ttp80) REVERT: G 137 HIS cc_start: 0.8198 (m90) cc_final: 0.7920 (m-70) REVERT: G 157 ILE cc_start: 0.9107 (mm) cc_final: 0.8787 (mm) REVERT: G 179 MET cc_start: 0.7840 (pp-130) cc_final: 0.7098 (ppp) REVERT: G 198 ASN cc_start: 0.9137 (m-40) cc_final: 0.8691 (m-40) REVERT: G 209 LEU cc_start: 0.7774 (tt) cc_final: 0.7566 (tt) REVERT: G 214 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7897 (tm-30) REVERT: G 272 VAL cc_start: 0.8926 (t) cc_final: 0.8541 (m) REVERT: G 277 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8577 (tm-30) REVERT: G 286 MET cc_start: 0.8942 (tmt) cc_final: 0.8329 (tmt) REVERT: G 319 ASP cc_start: 0.8222 (m-30) cc_final: 0.7781 (m-30) REVERT: G 327 SER cc_start: 0.8613 (p) cc_final: 0.8323 (p) REVERT: G 352 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8394 (tm-30) REVERT: G 412 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8015 (ptt90) REVERT: G 496 SER cc_start: 0.9134 (p) cc_final: 0.8909 (p) REVERT: G 507 HIS cc_start: 0.8564 (t-90) cc_final: 0.7915 (t-90) REVERT: H 16 ASP cc_start: 0.8374 (t0) cc_final: 0.8112 (t0) REVERT: H 28 ASP cc_start: 0.8245 (m-30) cc_final: 0.8017 (m-30) REVERT: H 75 GLU cc_start: 0.6947 (pm20) cc_final: 0.6552 (pm20) REVERT: H 105 ARG cc_start: 0.8280 (mtm110) cc_final: 0.8047 (ttp80) REVERT: H 137 HIS cc_start: 0.8215 (m90) cc_final: 0.7964 (m-70) REVERT: H 157 ILE cc_start: 0.9148 (mm) cc_final: 0.8826 (mm) REVERT: H 179 MET cc_start: 0.8062 (pp-130) cc_final: 0.7235 (ppp) REVERT: H 198 ASN cc_start: 0.9087 (m-40) cc_final: 0.8624 (m-40) REVERT: H 203 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8174 (ttp-110) REVERT: H 214 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8001 (tm-30) REVERT: H 272 VAL cc_start: 0.8927 (t) cc_final: 0.8604 (m) REVERT: H 277 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8364 (tm-30) REVERT: H 286 MET cc_start: 0.8977 (tmt) cc_final: 0.8481 (tmt) REVERT: H 319 ASP cc_start: 0.8184 (m-30) cc_final: 0.7938 (m-30) REVERT: H 327 SER cc_start: 0.8619 (p) cc_final: 0.8286 (p) REVERT: H 352 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8292 (tm-30) REVERT: H 412 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7993 (ptt90) REVERT: H 470 ASP cc_start: 0.8938 (m-30) cc_final: 0.8727 (m-30) REVERT: H 496 SER cc_start: 0.9093 (p) cc_final: 0.8802 (p) REVERT: H 507 HIS cc_start: 0.8540 (t-90) cc_final: 0.7894 (t-90) outliers start: 296 outliers final: 106 residues processed: 1203 average time/residue: 0.4512 time to fit residues: 844.1470 Evaluate side-chains 850 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 736 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 399 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 228 optimal weight: 0.7980 chunk 355 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 112 GLN A 198 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN B 93 HIS B 198 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS B 478 GLN C 112 GLN C 198 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS C 478 GLN D 198 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS D 478 GLN E 21 GLN E 25 ASN E 93 HIS E 112 GLN E 198 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS E 478 GLN F 198 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 GLN G 112 GLN G 198 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN H 93 HIS H 198 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS H 478 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32072 Z= 0.227 Angle : 0.742 8.140 43488 Z= 0.376 Chirality : 0.047 0.188 4968 Planarity : 0.004 0.067 5448 Dihedral : 15.645 78.412 5582 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.21 % Favored : 92.39 % Rotamer: Outliers : 6.39 % Allowed : 15.13 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -3.25 (0.12), residues: 3968 helix: -2.14 (0.12), residues: 1304 sheet: -1.88 (0.21), residues: 560 loop : -2.24 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 253 PHE 0.016 0.002 PHE F 401 TYR 0.012 0.001 TYR F 348 ARG 0.004 0.001 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 928 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8279 (t0) cc_final: 0.8052 (t0) REVERT: A 36 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 75 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: A 137 HIS cc_start: 0.8029 (m90) cc_final: 0.7652 (m-70) REVERT: A 174 PHE cc_start: 0.8325 (m-80) cc_final: 0.7962 (t80) REVERT: A 179 MET cc_start: 0.7672 (pp-130) cc_final: 0.6461 (ppp) REVERT: A 198 ASN cc_start: 0.9251 (m110) cc_final: 0.8654 (m-40) REVERT: A 202 GLN cc_start: 0.8339 (pp30) cc_final: 0.7820 (pp30) REVERT: A 214 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8038 (tm-30) REVERT: A 256 ASP cc_start: 0.8108 (p0) cc_final: 0.7766 (p0) REVERT: A 319 ASP cc_start: 0.8134 (m-30) cc_final: 0.7885 (m-30) REVERT: A 352 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 353 TYR cc_start: 0.8788 (t80) cc_final: 0.8534 (t80) REVERT: A 364 ASP cc_start: 0.7945 (p0) cc_final: 0.7582 (p0) REVERT: A 412 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7668 (ptt90) REVERT: A 474 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8538 (mtpt) REVERT: A 483 MET cc_start: 0.9263 (tmm) cc_final: 0.8721 (tmm) REVERT: A 507 HIS cc_start: 0.8498 (t-90) cc_final: 0.8030 (t-90) REVERT: B 16 ASP cc_start: 0.8261 (t0) cc_final: 0.8014 (t0) REVERT: B 36 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8246 (pp) REVERT: B 75 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6408 (pm20) REVERT: B 82 MET cc_start: 0.8742 (tpp) cc_final: 0.8518 (tpp) REVERT: B 94 ASN cc_start: 0.9175 (t0) cc_final: 0.8883 (t0) REVERT: B 179 MET cc_start: 0.7845 (pp-130) cc_final: 0.6642 (ppp) REVERT: B 198 ASN cc_start: 0.9274 (m110) cc_final: 0.8728 (m-40) REVERT: B 206 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7896 (mtmm) REVERT: B 214 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8183 (tm-30) REVERT: B 245 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8102 (mm) REVERT: B 256 ASP cc_start: 0.8221 (p0) cc_final: 0.7916 (p0) REVERT: B 319 ASP cc_start: 0.8130 (m-30) cc_final: 0.7804 (m-30) REVERT: B 352 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 353 TYR cc_start: 0.8857 (t80) cc_final: 0.8593 (t80) REVERT: B 412 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7697 (ptt90) REVERT: B 461 ILE cc_start: 0.8888 (pp) cc_final: 0.8562 (mt) REVERT: B 474 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8434 (mtpt) REVERT: B 507 HIS cc_start: 0.8519 (t-90) cc_final: 0.8103 (t-90) REVERT: C 16 ASP cc_start: 0.8273 (t0) cc_final: 0.7999 (t0) REVERT: C 34 ASP cc_start: 0.8956 (t0) cc_final: 0.8744 (t0) REVERT: C 36 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8082 (pp) REVERT: C 75 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: C 174 PHE cc_start: 0.8368 (m-80) cc_final: 0.8016 (t80) REVERT: C 179 MET cc_start: 0.7569 (pp-130) cc_final: 0.6459 (ppp) REVERT: C 198 ASN cc_start: 0.9268 (m110) cc_final: 0.8742 (m-40) REVERT: C 199 GLU cc_start: 0.7993 (pt0) cc_final: 0.7735 (tp30) REVERT: C 203 ARG cc_start: 0.8740 (tpp-160) cc_final: 0.8098 (mtp-110) REVERT: C 209 LEU cc_start: 0.8171 (tt) cc_final: 0.7962 (tt) REVERT: C 214 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8073 (tm-30) REVERT: C 261 ASP cc_start: 0.7969 (p0) cc_final: 0.6399 (p0) REVERT: C 262 LEU cc_start: 0.8682 (mt) cc_final: 0.7796 (mp) REVERT: C 319 ASP cc_start: 0.8269 (m-30) cc_final: 0.7833 (m-30) REVERT: C 352 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8307 (tm-30) REVERT: C 353 TYR cc_start: 0.8838 (t80) cc_final: 0.8609 (t80) REVERT: C 412 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7695 (ptt90) REVERT: C 474 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8407 (mtpt) REVERT: C 483 MET cc_start: 0.9269 (tmm) cc_final: 0.8765 (tmm) REVERT: C 507 HIS cc_start: 0.8536 (t-90) cc_final: 0.8102 (t-90) REVERT: D 16 ASP cc_start: 0.8296 (t0) cc_final: 0.8043 (t0) REVERT: D 36 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8292 (pp) REVERT: D 75 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: D 137 HIS cc_start: 0.8070 (m90) cc_final: 0.7720 (m-70) REVERT: D 174 PHE cc_start: 0.8187 (m-80) cc_final: 0.7418 (t80) REVERT: D 179 MET cc_start: 0.7896 (pp-130) cc_final: 0.6739 (ppp) REVERT: D 198 ASN cc_start: 0.9287 (m110) cc_final: 0.8765 (m-40) REVERT: D 214 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8162 (tm-30) REVERT: D 286 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8476 (tmt) REVERT: D 319 ASP cc_start: 0.8151 (m-30) cc_final: 0.7854 (m-30) REVERT: D 352 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 353 TYR cc_start: 0.8862 (t80) cc_final: 0.8627 (t80) REVERT: D 364 ASP cc_start: 0.7942 (p0) cc_final: 0.7618 (p0) REVERT: D 412 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7753 (ptt90) REVERT: D 474 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8455 (mtpt) REVERT: D 483 MET cc_start: 0.9222 (tmm) cc_final: 0.8638 (tmm) REVERT: D 507 HIS cc_start: 0.8551 (t-90) cc_final: 0.8108 (t-90) REVERT: E 36 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8213 (pp) REVERT: E 75 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6450 (pm20) REVERT: E 179 MET cc_start: 0.7673 (pp-130) cc_final: 0.6648 (ppp) REVERT: E 198 ASN cc_start: 0.9264 (m110) cc_final: 0.8716 (m-40) REVERT: E 199 GLU cc_start: 0.8009 (pt0) cc_final: 0.7688 (tp30) REVERT: E 202 GLN cc_start: 0.8238 (pp30) cc_final: 0.7821 (pp30) REVERT: E 203 ARG cc_start: 0.8689 (tpp-160) cc_final: 0.8042 (mtp-110) REVERT: E 205 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8425 (ttmm) REVERT: E 209 LEU cc_start: 0.8077 (tt) cc_final: 0.7849 (tt) REVERT: E 214 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8117 (tm-30) REVERT: E 245 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8075 (mm) REVERT: E 256 ASP cc_start: 0.8184 (p0) cc_final: 0.7908 (p0) REVERT: E 319 ASP cc_start: 0.8230 (m-30) cc_final: 0.7673 (m-30) REVERT: E 352 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8305 (tm-30) REVERT: E 412 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7727 (ptt90) REVERT: E 474 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8473 (mtpt) REVERT: E 483 MET cc_start: 0.9268 (tmm) cc_final: 0.8749 (tmm) REVERT: E 496 SER cc_start: 0.9086 (p) cc_final: 0.8811 (p) REVERT: E 507 HIS cc_start: 0.8536 (t-90) cc_final: 0.8154 (t-90) REVERT: F 16 ASP cc_start: 0.8282 (t0) cc_final: 0.7988 (t0) REVERT: F 34 ASP cc_start: 0.8964 (t0) cc_final: 0.8749 (t0) REVERT: F 75 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6518 (pm20) REVERT: F 174 PHE cc_start: 0.7989 (m-80) cc_final: 0.7318 (t80) REVERT: F 179 MET cc_start: 0.7772 (pp-130) cc_final: 0.6670 (ppp) REVERT: F 198 ASN cc_start: 0.9249 (m110) cc_final: 0.8738 (m-40) REVERT: F 199 GLU cc_start: 0.7977 (pt0) cc_final: 0.7620 (tp30) REVERT: F 202 GLN cc_start: 0.8253 (pp30) cc_final: 0.7848 (pp30) REVERT: F 203 ARG cc_start: 0.8616 (tpp-160) cc_final: 0.8019 (mtp-110) REVERT: F 205 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8500 (ttmm) REVERT: F 214 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8041 (tm-30) REVERT: F 286 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8421 (tmt) REVERT: F 319 ASP cc_start: 0.8129 (m-30) cc_final: 0.7785 (m-30) REVERT: F 352 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8285 (tm-30) REVERT: F 353 TYR cc_start: 0.8870 (t80) cc_final: 0.8631 (t80) REVERT: F 364 ASP cc_start: 0.7921 (p0) cc_final: 0.7621 (p0) REVERT: F 412 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7727 (ptt90) REVERT: F 474 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8463 (mtpt) REVERT: F 483 MET cc_start: 0.9214 (tmm) cc_final: 0.8659 (tmm) REVERT: F 507 HIS cc_start: 0.8549 (t-90) cc_final: 0.8118 (t-90) REVERT: G 16 ASP cc_start: 0.8302 (t0) cc_final: 0.8072 (t0) REVERT: G 36 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8096 (pp) REVERT: G 75 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6510 (pm20) REVERT: G 92 HIS cc_start: 0.9196 (p90) cc_final: 0.8785 (p90) REVERT: G 174 PHE cc_start: 0.8072 (m-80) cc_final: 0.7858 (t80) REVERT: G 179 MET cc_start: 0.7653 (pp-130) cc_final: 0.6431 (ppp) REVERT: G 198 ASN cc_start: 0.9264 (m110) cc_final: 0.8752 (m-40) REVERT: G 199 GLU cc_start: 0.8009 (pt0) cc_final: 0.7754 (tp30) REVERT: G 202 GLN cc_start: 0.8343 (pp30) cc_final: 0.8016 (pp30) REVERT: G 203 ARG cc_start: 0.8741 (tpp-160) cc_final: 0.7957 (mtp-110) REVERT: G 205 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8479 (ttmm) REVERT: G 214 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8015 (tm-30) REVERT: G 261 ASP cc_start: 0.7962 (p0) cc_final: 0.6665 (p0) REVERT: G 286 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8432 (tmt) REVERT: G 319 ASP cc_start: 0.8159 (m-30) cc_final: 0.7881 (m-30) REVERT: G 352 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8285 (tm-30) REVERT: G 364 ASP cc_start: 0.7910 (p0) cc_final: 0.7593 (p0) REVERT: G 412 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7571 (ptt90) REVERT: G 474 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8486 (mtpt) REVERT: G 507 HIS cc_start: 0.8518 (t-90) cc_final: 0.8044 (t-90) REVERT: H 16 ASP cc_start: 0.8414 (t0) cc_final: 0.8171 (t0) REVERT: H 36 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8265 (pp) REVERT: H 75 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: H 179 MET cc_start: 0.7965 (pp-130) cc_final: 0.6856 (ppp) REVERT: H 198 ASN cc_start: 0.9259 (m110) cc_final: 0.8740 (m-40) REVERT: H 202 GLN cc_start: 0.8308 (pp30) cc_final: 0.7847 (pp30) REVERT: H 205 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8403 (ttmm) REVERT: H 214 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8135 (tm-30) REVERT: H 286 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8435 (tmt) REVERT: H 319 ASP cc_start: 0.8113 (m-30) cc_final: 0.7801 (m-30) REVERT: H 352 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8224 (tm-30) REVERT: H 353 TYR cc_start: 0.8825 (t80) cc_final: 0.8573 (t80) REVERT: H 364 ASP cc_start: 0.7961 (p0) cc_final: 0.7638 (p0) REVERT: H 412 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7716 (ptt90) REVERT: H 474 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8476 (mtpt) REVERT: H 483 MET cc_start: 0.9242 (tmm) cc_final: 0.8707 (tmm) REVERT: H 507 HIS cc_start: 0.8523 (t-90) cc_final: 0.8112 (t-90) outliers start: 209 outliers final: 119 residues processed: 1052 average time/residue: 0.4368 time to fit residues: 736.5895 Evaluate side-chains 879 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 739 time to evaluate : 3.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 296 optimal weight: 0.9980 chunk 242 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 356 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 286 optimal weight: 0.2980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS D 21 GLN D 25 ASN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS E 102 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS F 21 GLN F 25 ASN F 92 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 25 ASN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 GLN H 25 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32072 Z= 0.333 Angle : 0.749 7.906 43488 Z= 0.381 Chirality : 0.048 0.179 4968 Planarity : 0.004 0.065 5448 Dihedral : 14.801 74.563 5448 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.64 % Favored : 91.15 % Rotamer: Outliers : 6.05 % Allowed : 18.34 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.66 (0.13), residues: 3968 helix: -1.31 (0.13), residues: 1288 sheet: -1.76 (0.20), residues: 616 loop : -2.05 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 253 PHE 0.016 0.002 PHE F 401 TYR 0.013 0.001 TYR A 348 ARG 0.004 0.001 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 791 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8261 (t0) cc_final: 0.8054 (t0) REVERT: A 36 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8313 (pp) REVERT: A 75 GLU cc_start: 0.6922 (pm20) cc_final: 0.6369 (pm20) REVERT: A 108 LYS cc_start: 0.8622 (tptp) cc_final: 0.8300 (tppt) REVERT: A 137 HIS cc_start: 0.8115 (m90) cc_final: 0.7678 (m-70) REVERT: A 174 PHE cc_start: 0.8206 (m-80) cc_final: 0.7713 (t80) REVERT: A 179 MET cc_start: 0.7730 (pp-130) cc_final: 0.6509 (ppp) REVERT: A 198 ASN cc_start: 0.9248 (m110) cc_final: 0.8747 (m-40) REVERT: A 205 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8596 (mmmm) REVERT: A 214 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8072 (tm-30) REVERT: A 319 ASP cc_start: 0.8226 (m-30) cc_final: 0.7827 (m-30) REVERT: A 352 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8295 (tm-30) REVERT: A 353 TYR cc_start: 0.8860 (t80) cc_final: 0.8638 (t80) REVERT: A 412 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7589 (ptt90) REVERT: A 474 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8582 (mtpt) REVERT: A 507 HIS cc_start: 0.8520 (t-90) cc_final: 0.8055 (t-90) REVERT: B 16 ASP cc_start: 0.8221 (t0) cc_final: 0.7981 (t0) REVERT: B 36 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8385 (pp) REVERT: B 75 GLU cc_start: 0.7015 (pm20) cc_final: 0.6474 (pm20) REVERT: B 108 LYS cc_start: 0.8532 (tptp) cc_final: 0.8176 (tppt) REVERT: B 179 MET cc_start: 0.7833 (pp-130) cc_final: 0.6677 (ppp) REVERT: B 198 ASN cc_start: 0.9238 (m110) cc_final: 0.8678 (m-40) REVERT: B 214 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8238 (tm-30) REVERT: B 244 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8261 (mt) REVERT: B 245 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8132 (mm) REVERT: B 319 ASP cc_start: 0.8205 (m-30) cc_final: 0.7803 (m-30) REVERT: B 352 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8317 (tm-30) REVERT: B 412 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7671 (ptt90) REVERT: B 461 ILE cc_start: 0.8926 (pp) cc_final: 0.8660 (mt) REVERT: B 474 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8468 (mtpt) REVERT: B 507 HIS cc_start: 0.8500 (t-90) cc_final: 0.8040 (t-90) REVERT: C 16 ASP cc_start: 0.8179 (t0) cc_final: 0.7938 (t0) REVERT: C 34 ASP cc_start: 0.9089 (t0) cc_final: 0.8694 (t0) REVERT: C 36 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8239 (pp) REVERT: C 63 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8805 (t) REVERT: C 75 GLU cc_start: 0.7034 (pm20) cc_final: 0.6498 (pm20) REVERT: C 108 LYS cc_start: 0.8651 (tptp) cc_final: 0.8254 (tppt) REVERT: C 174 PHE cc_start: 0.8242 (m-80) cc_final: 0.7810 (t80) REVERT: C 179 MET cc_start: 0.7523 (pp-130) cc_final: 0.6365 (ppp) REVERT: C 198 ASN cc_start: 0.9222 (m110) cc_final: 0.8720 (m-40) REVERT: C 199 GLU cc_start: 0.8113 (pt0) cc_final: 0.7804 (tp30) REVERT: C 203 ARG cc_start: 0.8848 (tpp-160) cc_final: 0.8266 (mtp-110) REVERT: C 209 LEU cc_start: 0.8112 (tt) cc_final: 0.7908 (tt) REVERT: C 214 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8082 (tm-30) REVERT: C 319 ASP cc_start: 0.8282 (m-30) cc_final: 0.7897 (m-30) REVERT: C 352 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8294 (tm-30) REVERT: C 353 TYR cc_start: 0.8878 (t80) cc_final: 0.8655 (t80) REVERT: C 412 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7366 (tmm-80) REVERT: C 474 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8516 (mtpt) REVERT: C 507 HIS cc_start: 0.8535 (t-90) cc_final: 0.8071 (t-90) REVERT: D 16 ASP cc_start: 0.8210 (t0) cc_final: 0.7944 (t0) REVERT: D 36 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8379 (pp) REVERT: D 63 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8874 (t) REVERT: D 75 GLU cc_start: 0.6962 (pm20) cc_final: 0.6450 (pm20) REVERT: D 92 HIS cc_start: 0.9034 (p90) cc_final: 0.8666 (p90) REVERT: D 108 LYS cc_start: 0.8609 (tptp) cc_final: 0.8288 (tppt) REVERT: D 137 HIS cc_start: 0.8131 (m90) cc_final: 0.7715 (m-70) REVERT: D 174 PHE cc_start: 0.8191 (m-80) cc_final: 0.7569 (t80) REVERT: D 179 MET cc_start: 0.7907 (pp-130) cc_final: 0.6737 (ppp) REVERT: D 198 ASN cc_start: 0.9291 (m110) cc_final: 0.8762 (m-40) REVERT: D 205 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8280 (ttmm) REVERT: D 214 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8169 (tm-30) REVERT: D 286 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8473 (tmt) REVERT: D 319 ASP cc_start: 0.8228 (m-30) cc_final: 0.7794 (m-30) REVERT: D 412 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7333 (tmm-80) REVERT: D 474 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8520 (mtpt) REVERT: D 507 HIS cc_start: 0.8548 (t-90) cc_final: 0.8072 (t-90) REVERT: E 36 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8310 (pp) REVERT: E 75 GLU cc_start: 0.7081 (pm20) cc_final: 0.6522 (pm20) REVERT: E 174 PHE cc_start: 0.8038 (m-80) cc_final: 0.7599 (t80) REVERT: E 179 MET cc_start: 0.7719 (pp-130) cc_final: 0.6490 (ppp) REVERT: E 198 ASN cc_start: 0.9224 (m110) cc_final: 0.8674 (m-40) REVERT: E 199 GLU cc_start: 0.8049 (pt0) cc_final: 0.7688 (tp30) REVERT: E 202 GLN cc_start: 0.8335 (pp30) cc_final: 0.7870 (pp30) REVERT: E 203 ARG cc_start: 0.8716 (tpp-160) cc_final: 0.8154 (mtp-110) REVERT: E 209 LEU cc_start: 0.8063 (tt) cc_final: 0.7817 (tt) REVERT: E 214 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8095 (tm-30) REVERT: E 231 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7791 (mmp80) REVERT: E 245 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8103 (mm) REVERT: E 319 ASP cc_start: 0.8230 (m-30) cc_final: 0.7761 (m-30) REVERT: E 352 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8308 (tm-30) REVERT: E 412 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7340 (tmm-80) REVERT: E 474 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8508 (mtpt) REVERT: E 507 HIS cc_start: 0.8545 (t-90) cc_final: 0.8116 (t-90) REVERT: F 16 ASP cc_start: 0.8198 (t0) cc_final: 0.7894 (t0) REVERT: F 63 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8858 (t) REVERT: F 75 GLU cc_start: 0.7039 (pm20) cc_final: 0.6517 (pm20) REVERT: F 108 LYS cc_start: 0.8611 (tptp) cc_final: 0.8278 (tppt) REVERT: F 174 PHE cc_start: 0.8032 (m-80) cc_final: 0.7367 (t80) REVERT: F 179 MET cc_start: 0.7826 (pp-130) cc_final: 0.6694 (ppp) REVERT: F 198 ASN cc_start: 0.9258 (m110) cc_final: 0.8755 (m-40) REVERT: F 199 GLU cc_start: 0.8101 (pt0) cc_final: 0.7820 (tp30) REVERT: F 202 GLN cc_start: 0.8283 (pp30) cc_final: 0.7794 (pp30) REVERT: F 205 LYS cc_start: 0.8775 (mmmm) cc_final: 0.8414 (ttmm) REVERT: F 214 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8099 (tm-30) REVERT: F 286 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8502 (tmt) REVERT: F 319 ASP cc_start: 0.8180 (m-30) cc_final: 0.7707 (m-30) REVERT: F 352 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8313 (tm-30) REVERT: F 353 TYR cc_start: 0.8913 (t80) cc_final: 0.8698 (t80) REVERT: F 412 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7353 (tmm-80) REVERT: F 507 HIS cc_start: 0.8546 (t-90) cc_final: 0.8079 (t-90) REVERT: G 16 ASP cc_start: 0.8221 (t0) cc_final: 0.7999 (t0) REVERT: G 28 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7876 (m-30) REVERT: G 36 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8269 (pp) REVERT: G 75 GLU cc_start: 0.7056 (pm20) cc_final: 0.6524 (pm20) REVERT: G 108 LYS cc_start: 0.8620 (tptp) cc_final: 0.8284 (tppt) REVERT: G 174 PHE cc_start: 0.8138 (m-80) cc_final: 0.7736 (t80) REVERT: G 179 MET cc_start: 0.7653 (pp-130) cc_final: 0.6399 (ppp) REVERT: G 198 ASN cc_start: 0.9227 (m110) cc_final: 0.8738 (m-40) REVERT: G 199 GLU cc_start: 0.8109 (pt0) cc_final: 0.7740 (tp30) REVERT: G 203 ARG cc_start: 0.8856 (tpp-160) cc_final: 0.8135 (mtp-110) REVERT: G 214 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8021 (tm-30) REVERT: G 286 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8457 (tmt) REVERT: G 319 ASP cc_start: 0.8256 (m-30) cc_final: 0.7808 (m-30) REVERT: G 352 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8307 (tm-30) REVERT: G 412 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7746 (ptt90) REVERT: G 474 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8568 (mtpt) REVERT: G 487 GLU cc_start: 0.8498 (tt0) cc_final: 0.8017 (tt0) REVERT: G 507 HIS cc_start: 0.8543 (t-90) cc_final: 0.8076 (t-90) REVERT: H 16 ASP cc_start: 0.8346 (t0) cc_final: 0.8105 (t0) REVERT: H 36 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8466 (pp) REVERT: H 75 GLU cc_start: 0.7000 (pm20) cc_final: 0.6492 (pm20) REVERT: H 108 LYS cc_start: 0.8547 (tptp) cc_final: 0.8173 (tppt) REVERT: H 132 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8374 (pp20) REVERT: H 179 MET cc_start: 0.7971 (pp-130) cc_final: 0.6854 (ppp) REVERT: H 198 ASN cc_start: 0.9229 (m110) cc_final: 0.8687 (m-40) REVERT: H 214 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8118 (tm-30) REVERT: H 286 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8514 (tmt) REVERT: H 319 ASP cc_start: 0.8181 (m-30) cc_final: 0.7749 (m-30) REVERT: H 412 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7702 (ptt90) REVERT: H 474 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8516 (mtpt) REVERT: H 507 HIS cc_start: 0.8521 (t-90) cc_final: 0.8071 (t-90) outliers start: 198 outliers final: 156 residues processed: 913 average time/residue: 0.3961 time to fit residues: 586.0468 Evaluate side-chains 906 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 731 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Chi-restraints excluded: chain H residue 499 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 239 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 chunk 378 optimal weight: 0.0170 chunk 186 optimal weight: 0.9980 chunk 339 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 198 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 198 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 198 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32072 Z= 0.205 Angle : 0.660 8.138 43488 Z= 0.336 Chirality : 0.045 0.145 4968 Planarity : 0.003 0.039 5448 Dihedral : 13.808 74.337 5407 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.64 % Favored : 92.16 % Rotamer: Outliers : 6.14 % Allowed : 22.16 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.25 (0.13), residues: 3968 helix: -0.81 (0.14), residues: 1312 sheet: -1.43 (0.23), residues: 480 loop : -1.97 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 253 PHE 0.012 0.001 PHE C 24 TYR 0.010 0.001 TYR D 411 ARG 0.005 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 843 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8190 (t0) cc_final: 0.7929 (t0) REVERT: A 36 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8146 (pp) REVERT: A 75 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: A 134 LYS cc_start: 0.8118 (pttp) cc_final: 0.7782 (pttm) REVERT: A 136 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.8223 (ptt180) REVERT: A 174 PHE cc_start: 0.8213 (m-80) cc_final: 0.7911 (t80) REVERT: A 179 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6314 (ppp) REVERT: A 198 ASN cc_start: 0.9287 (m-40) cc_final: 0.8719 (m-40) REVERT: A 203 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8199 (mtp-110) REVERT: A 214 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8146 (tm-30) REVERT: A 277 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7846 (tm-30) REVERT: A 319 ASP cc_start: 0.8163 (m-30) cc_final: 0.7837 (m-30) REVERT: A 412 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7479 (ptt90) REVERT: A 441 GLN cc_start: 0.8563 (tt0) cc_final: 0.8334 (mt0) REVERT: A 474 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8516 (mtpt) REVERT: A 507 HIS cc_start: 0.8520 (t-90) cc_final: 0.8047 (t-90) REVERT: B 16 ASP cc_start: 0.8172 (t0) cc_final: 0.7856 (t0) REVERT: B 75 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: B 82 MET cc_start: 0.8957 (tpp) cc_final: 0.8739 (tpp) REVERT: B 134 LYS cc_start: 0.8204 (pttp) cc_final: 0.7798 (pttm) REVERT: B 179 MET cc_start: 0.7775 (pp-130) cc_final: 0.6670 (ppp) REVERT: B 198 ASN cc_start: 0.9280 (m-40) cc_final: 0.8648 (m-40) REVERT: B 205 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8306 (ttmm) REVERT: B 214 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8318 (tm-30) REVERT: B 245 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8130 (mm) REVERT: B 259 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8045 (mtp180) REVERT: B 319 ASP cc_start: 0.8176 (m-30) cc_final: 0.7827 (m-30) REVERT: B 379 LEU cc_start: 0.9523 (mt) cc_final: 0.9323 (mt) REVERT: B 412 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7552 (ptt90) REVERT: B 474 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8428 (mtpt) REVERT: B 507 HIS cc_start: 0.8461 (t-90) cc_final: 0.8018 (t-90) REVERT: C 16 ASP cc_start: 0.8165 (t0) cc_final: 0.7907 (t0) REVERT: C 34 ASP cc_start: 0.8924 (t0) cc_final: 0.8652 (t0) REVERT: C 36 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8203 (pp) REVERT: C 75 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: C 108 LYS cc_start: 0.8517 (tptp) cc_final: 0.8074 (tppt) REVERT: C 134 LYS cc_start: 0.8188 (pttp) cc_final: 0.7801 (pttm) REVERT: C 136 ARG cc_start: 0.8522 (ptm-80) cc_final: 0.8261 (ptt180) REVERT: C 150 MET cc_start: 0.8133 (ttt) cc_final: 0.7775 (tpp) REVERT: C 174 PHE cc_start: 0.8279 (m-80) cc_final: 0.7982 (t80) REVERT: C 179 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6466 (ppp) REVERT: C 198 ASN cc_start: 0.9263 (m-40) cc_final: 0.8678 (m-40) REVERT: C 199 GLU cc_start: 0.8015 (pt0) cc_final: 0.7713 (tp30) REVERT: C 202 GLN cc_start: 0.8374 (pp30) cc_final: 0.8030 (pp30) REVERT: C 203 ARG cc_start: 0.8859 (tpp-160) cc_final: 0.8267 (mtp-110) REVERT: C 214 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8133 (tm-30) REVERT: C 286 MET cc_start: 0.8957 (tpp) cc_final: 0.8683 (tpp) REVERT: C 352 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8275 (tm-30) REVERT: C 353 TYR cc_start: 0.8736 (t80) cc_final: 0.8512 (t80) REVERT: C 412 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7547 (ptt90) REVERT: C 474 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8508 (mtpt) REVERT: C 507 HIS cc_start: 0.8508 (t-90) cc_final: 0.8075 (t-90) REVERT: D 16 ASP cc_start: 0.8203 (t0) cc_final: 0.7890 (t0) REVERT: D 75 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: D 82 MET cc_start: 0.8957 (tpp) cc_final: 0.8750 (tpp) REVERT: D 134 LYS cc_start: 0.8042 (pttp) cc_final: 0.7675 (pttm) REVERT: D 136 ARG cc_start: 0.8587 (ptm-80) cc_final: 0.8315 (ptt180) REVERT: D 150 MET cc_start: 0.8137 (ttt) cc_final: 0.7779 (tpp) REVERT: D 174 PHE cc_start: 0.8147 (m-80) cc_final: 0.7582 (t80) REVERT: D 179 MET cc_start: 0.7817 (pp-130) cc_final: 0.6697 (ppp) REVERT: D 205 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8263 (ttmm) REVERT: D 214 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8221 (tm-30) REVERT: D 259 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8099 (mtp180) REVERT: D 277 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7899 (tm-30) REVERT: D 286 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8484 (tmt) REVERT: D 319 ASP cc_start: 0.8181 (m-30) cc_final: 0.7858 (m-30) REVERT: D 412 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7635 (ptt90) REVERT: D 474 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8463 (mtpt) REVERT: D 507 HIS cc_start: 0.8522 (t-90) cc_final: 0.8100 (t-90) REVERT: E 34 ASP cc_start: 0.8864 (t0) cc_final: 0.8625 (t0) REVERT: E 75 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: E 82 MET cc_start: 0.8987 (tpp) cc_final: 0.8772 (tpp) REVERT: E 134 LYS cc_start: 0.8273 (pttp) cc_final: 0.7883 (pttm) REVERT: E 136 ARG cc_start: 0.8534 (ptm160) cc_final: 0.8195 (ptt180) REVERT: E 150 MET cc_start: 0.8050 (ttt) cc_final: 0.7735 (tpp) REVERT: E 179 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6366 (ppp) REVERT: E 198 ASN cc_start: 0.9271 (m-40) cc_final: 0.8637 (m-40) REVERT: E 199 GLU cc_start: 0.8017 (pt0) cc_final: 0.7664 (tp30) REVERT: E 202 GLN cc_start: 0.8482 (pp30) cc_final: 0.8046 (pp30) REVERT: E 203 ARG cc_start: 0.8779 (tpp-160) cc_final: 0.8094 (mtp-110) REVERT: E 209 LEU cc_start: 0.8073 (tt) cc_final: 0.7825 (tt) REVERT: E 214 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8129 (tm-30) REVERT: E 231 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7755 (mmp80) REVERT: E 245 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8058 (mm) REVERT: E 300 ILE cc_start: 0.8245 (mm) cc_final: 0.8016 (mm) REVERT: E 319 ASP cc_start: 0.8147 (m-30) cc_final: 0.7743 (m-30) REVERT: E 352 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8257 (tm-30) REVERT: E 379 LEU cc_start: 0.9502 (mt) cc_final: 0.9197 (mt) REVERT: E 412 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7558 (ptt90) REVERT: E 474 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8404 (mtpt) REVERT: E 483 MET cc_start: 0.9301 (tmm) cc_final: 0.8799 (tmm) REVERT: E 507 HIS cc_start: 0.8517 (t-90) cc_final: 0.8109 (t-90) REVERT: F 16 ASP cc_start: 0.8181 (t0) cc_final: 0.7906 (t0) REVERT: F 75 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6570 (pm20) REVERT: F 92 HIS cc_start: 0.8922 (p90) cc_final: 0.8622 (p-80) REVERT: F 108 LYS cc_start: 0.8528 (tptp) cc_final: 0.8095 (tppt) REVERT: F 136 ARG cc_start: 0.8644 (ptm-80) cc_final: 0.8291 (ptt180) REVERT: F 150 MET cc_start: 0.8038 (ttt) cc_final: 0.7780 (tpp) REVERT: F 179 MET cc_start: 0.7784 (pp-130) cc_final: 0.6694 (ppp) REVERT: F 199 GLU cc_start: 0.8087 (pt0) cc_final: 0.7664 (tp30) REVERT: F 202 GLN cc_start: 0.8428 (pp30) cc_final: 0.7982 (pp30) REVERT: F 203 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8148 (mtp-110) REVERT: F 214 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8081 (tm-30) REVERT: F 286 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8483 (tmt) REVERT: F 319 ASP cc_start: 0.8110 (m-30) cc_final: 0.7719 (m-30) REVERT: F 409 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8219 (tppt) REVERT: F 412 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7683 (ptt90) REVERT: F 507 HIS cc_start: 0.8524 (t-90) cc_final: 0.8111 (t-90) REVERT: G 16 ASP cc_start: 0.8206 (t0) cc_final: 0.7941 (t0) REVERT: G 75 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: G 92 HIS cc_start: 0.9022 (p90) cc_final: 0.8764 (p-80) REVERT: G 132 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8335 (pp20) REVERT: G 136 ARG cc_start: 0.8575 (ptm-80) cc_final: 0.8259 (ptt180) REVERT: G 174 PHE cc_start: 0.8162 (m-80) cc_final: 0.7887 (t80) REVERT: G 179 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6268 (ppp) REVERT: G 198 ASN cc_start: 0.9269 (m-40) cc_final: 0.8737 (m-40) REVERT: G 199 GLU cc_start: 0.8077 (pt0) cc_final: 0.7828 (tp30) REVERT: G 202 GLN cc_start: 0.8405 (pp30) cc_final: 0.8079 (pp30) REVERT: G 203 ARG cc_start: 0.8883 (tpp-160) cc_final: 0.8152 (mtp-110) REVERT: G 214 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8099 (tm-30) REVERT: G 256 ASP cc_start: 0.8284 (p0) cc_final: 0.7599 (p0) REVERT: G 277 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8042 (tm-30) REVERT: G 412 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7543 (ptt90) REVERT: G 474 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8537 (mtpt) REVERT: G 507 HIS cc_start: 0.8523 (t-90) cc_final: 0.8045 (t-90) REVERT: H 16 ASP cc_start: 0.8175 (t0) cc_final: 0.7869 (t0) REVERT: H 75 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6581 (pm20) REVERT: H 92 HIS cc_start: 0.9081 (p90) cc_final: 0.8702 (p90) REVERT: H 132 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8425 (pp20) REVERT: H 134 LYS cc_start: 0.8049 (pttp) cc_final: 0.7592 (pttm) REVERT: H 136 ARG cc_start: 0.8579 (ptm-80) cc_final: 0.8288 (ptt180) REVERT: H 179 MET cc_start: 0.7794 (pp-130) cc_final: 0.6718 (ppp) REVERT: H 214 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8160 (tm-30) REVERT: H 259 ARG cc_start: 0.8389 (mtp85) cc_final: 0.7947 (mtp180) REVERT: H 261 ASP cc_start: 0.8100 (p0) cc_final: 0.7710 (p0) REVERT: H 319 ASP cc_start: 0.8099 (m-30) cc_final: 0.7709 (m-30) REVERT: H 379 LEU cc_start: 0.9521 (mt) cc_final: 0.9316 (mt) REVERT: H 409 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8156 (tppt) REVERT: H 412 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7590 (ptt90) REVERT: H 474 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8493 (mtpt) REVERT: H 507 HIS cc_start: 0.8505 (t-90) cc_final: 0.8081 (t-90) outliers start: 201 outliers final: 130 residues processed: 961 average time/residue: 0.4432 time to fit residues: 691.8863 Evaluate side-chains 896 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 746 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 282 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 323 optimal weight: 0.6980 chunk 261 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32072 Z= 0.227 Angle : 0.665 8.395 43488 Z= 0.337 Chirality : 0.046 0.142 4968 Planarity : 0.004 0.076 5448 Dihedral : 13.421 75.838 5402 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.48 % Allowed : 22.56 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.01 (0.13), residues: 3968 helix: -0.56 (0.14), residues: 1280 sheet: -1.23 (0.23), residues: 480 loop : -1.86 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS H 253 PHE 0.013 0.001 PHE A 24 TYR 0.010 0.001 TYR G 348 ARG 0.005 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 805 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8198 (t0) cc_final: 0.7943 (t0) REVERT: A 36 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8167 (pp) REVERT: A 75 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: A 134 LYS cc_start: 0.8001 (pttp) cc_final: 0.7710 (pttm) REVERT: A 136 ARG cc_start: 0.8511 (ptm-80) cc_final: 0.8002 (ptt90) REVERT: A 174 PHE cc_start: 0.8188 (m-80) cc_final: 0.7784 (t80) REVERT: A 179 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.6415 (ppp) REVERT: A 203 ARG cc_start: 0.8772 (tpp-160) cc_final: 0.8263 (mtp-110) REVERT: A 214 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8144 (tm-30) REVERT: A 231 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7738 (mmm160) REVERT: A 259 ARG cc_start: 0.8492 (mtp85) cc_final: 0.7966 (mtp180) REVERT: A 300 ILE cc_start: 0.8358 (mm) cc_final: 0.7842 (mt) REVERT: A 319 ASP cc_start: 0.8182 (m-30) cc_final: 0.7805 (m-30) REVERT: A 412 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7450 (ptt90) REVERT: A 474 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8456 (mtpt) REVERT: A 507 HIS cc_start: 0.8537 (t-90) cc_final: 0.8091 (t-90) REVERT: B 16 ASP cc_start: 0.8166 (t0) cc_final: 0.7902 (t0) REVERT: B 34 ASP cc_start: 0.8964 (t0) cc_final: 0.8678 (t0) REVERT: B 75 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: B 134 LYS cc_start: 0.8145 (pttp) cc_final: 0.7806 (pttm) REVERT: B 179 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.6710 (ppp) REVERT: B 198 ASN cc_start: 0.9275 (m-40) cc_final: 0.8735 (m-40) REVERT: B 205 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8242 (ttmm) REVERT: B 214 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8305 (tm-30) REVERT: B 245 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8162 (mm) REVERT: B 259 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8021 (mtp180) REVERT: B 319 ASP cc_start: 0.8111 (m-30) cc_final: 0.7746 (m-30) REVERT: B 379 LEU cc_start: 0.9473 (mt) cc_final: 0.9238 (mt) REVERT: B 412 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7505 (ptt90) REVERT: B 474 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8435 (mtpt) REVERT: B 507 HIS cc_start: 0.8483 (t-90) cc_final: 0.8025 (t-90) REVERT: C 16 ASP cc_start: 0.8173 (t0) cc_final: 0.7900 (t0) REVERT: C 34 ASP cc_start: 0.8972 (t0) cc_final: 0.8661 (t0) REVERT: C 36 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8179 (pp) REVERT: C 75 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: C 134 LYS cc_start: 0.8065 (pttp) cc_final: 0.7754 (pttm) REVERT: C 136 ARG cc_start: 0.8551 (ptm-80) cc_final: 0.8039 (ptt90) REVERT: C 150 MET cc_start: 0.8132 (ttt) cc_final: 0.7842 (tpp) REVERT: C 174 PHE cc_start: 0.8173 (m-80) cc_final: 0.7717 (t80) REVERT: C 179 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6367 (ppp) REVERT: C 199 GLU cc_start: 0.8095 (pt0) cc_final: 0.7781 (tp30) REVERT: C 203 ARG cc_start: 0.8880 (tpp-160) cc_final: 0.8294 (mtp-110) REVERT: C 214 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8138 (tm-30) REVERT: C 231 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7670 (mmm160) REVERT: C 286 MET cc_start: 0.9006 (tpp) cc_final: 0.8669 (tpp) REVERT: C 352 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8271 (tm-30) REVERT: C 353 TYR cc_start: 0.8784 (t80) cc_final: 0.8539 (t80) REVERT: C 412 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7558 (ptt90) REVERT: C 474 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8445 (mtpt) REVERT: C 507 HIS cc_start: 0.8535 (t-90) cc_final: 0.8107 (t-90) REVERT: D 16 ASP cc_start: 0.8194 (t0) cc_final: 0.7946 (t0) REVERT: D 75 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6361 (pm20) REVERT: D 134 LYS cc_start: 0.7984 (pttp) cc_final: 0.7656 (pttm) REVERT: D 136 ARG cc_start: 0.8596 (ptm-80) cc_final: 0.8313 (ptt180) REVERT: D 150 MET cc_start: 0.8115 (ttt) cc_final: 0.7810 (tpp) REVERT: D 174 PHE cc_start: 0.8142 (m-80) cc_final: 0.7624 (t80) REVERT: D 179 MET cc_start: 0.7817 (pp-130) cc_final: 0.6707 (ppp) REVERT: D 214 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8234 (tm-30) REVERT: D 319 ASP cc_start: 0.8170 (m-30) cc_final: 0.7749 (m-30) REVERT: D 412 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7591 (ptt90) REVERT: D 474 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8426 (mtpt) REVERT: D 507 HIS cc_start: 0.8549 (t-90) cc_final: 0.8128 (t-90) REVERT: E 16 ASP cc_start: 0.8040 (t0) cc_final: 0.7815 (t0) REVERT: E 34 ASP cc_start: 0.8937 (t0) cc_final: 0.8601 (t0) REVERT: E 75 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: E 134 LYS cc_start: 0.8221 (pttp) cc_final: 0.7873 (pttm) REVERT: E 136 ARG cc_start: 0.8529 (ptm160) cc_final: 0.8184 (ptt180) REVERT: E 150 MET cc_start: 0.8034 (ttt) cc_final: 0.7830 (tpp) REVERT: E 179 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6417 (ppp) REVERT: E 198 ASN cc_start: 0.9282 (m-40) cc_final: 0.8755 (m-40) REVERT: E 199 GLU cc_start: 0.8035 (pt0) cc_final: 0.7658 (tp30) REVERT: E 202 GLN cc_start: 0.8510 (pp30) cc_final: 0.8096 (pp30) REVERT: E 203 ARG cc_start: 0.8755 (tpp-160) cc_final: 0.8140 (mtp-110) REVERT: E 214 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8138 (tm-30) REVERT: E 231 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7767 (mmp80) REVERT: E 245 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8104 (mm) REVERT: E 259 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8031 (mtp180) REVERT: E 300 ILE cc_start: 0.8311 (mm) cc_final: 0.8058 (mm) REVERT: E 319 ASP cc_start: 0.8169 (m-30) cc_final: 0.7687 (m-30) REVERT: E 379 LEU cc_start: 0.9533 (mt) cc_final: 0.9278 (mt) REVERT: E 412 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7513 (ptt90) REVERT: E 474 LYS cc_start: 0.8646 (mtpt) cc_final: 0.8418 (mtpt) REVERT: E 507 HIS cc_start: 0.8536 (t-90) cc_final: 0.8154 (t-90) REVERT: F 16 ASP cc_start: 0.8178 (t0) cc_final: 0.7926 (t0) REVERT: F 75 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: F 92 HIS cc_start: 0.8956 (p90) cc_final: 0.8686 (p-80) REVERT: F 134 LYS cc_start: 0.7918 (pttp) cc_final: 0.7527 (pttm) REVERT: F 136 ARG cc_start: 0.8624 (ptm-80) cc_final: 0.8335 (ptt180) REVERT: F 150 MET cc_start: 0.8064 (ttt) cc_final: 0.7825 (tpp) REVERT: F 179 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.6761 (ppp) REVERT: F 199 GLU cc_start: 0.8140 (pt0) cc_final: 0.7726 (tp30) REVERT: F 202 GLN cc_start: 0.8534 (pp30) cc_final: 0.8059 (pp30) REVERT: F 203 ARG cc_start: 0.8712 (tpp-160) cc_final: 0.8098 (mtp-110) REVERT: F 214 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8095 (tm-30) REVERT: F 286 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8495 (tmt) REVERT: F 319 ASP cc_start: 0.8118 (m-30) cc_final: 0.7703 (m-30) REVERT: F 409 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8278 (tppt) REVERT: F 412 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7673 (ptt90) REVERT: F 507 HIS cc_start: 0.8556 (t-90) cc_final: 0.8147 (t-90) REVERT: G 16 ASP cc_start: 0.8220 (t0) cc_final: 0.7989 (t0) REVERT: G 75 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: G 92 HIS cc_start: 0.9025 (p90) cc_final: 0.8743 (p-80) REVERT: G 132 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8369 (pp20) REVERT: G 134 LYS cc_start: 0.8054 (pttp) cc_final: 0.7660 (pttm) REVERT: G 136 ARG cc_start: 0.8577 (ptm-80) cc_final: 0.8133 (ptt180) REVERT: G 174 PHE cc_start: 0.8185 (m-80) cc_final: 0.7784 (t80) REVERT: G 179 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.6274 (ppp) REVERT: G 199 GLU cc_start: 0.8102 (pt0) cc_final: 0.7741 (tp30) REVERT: G 203 ARG cc_start: 0.8893 (tpp-160) cc_final: 0.8197 (mtp-110) REVERT: G 214 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8103 (tm-30) REVERT: G 231 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7700 (mmm160) REVERT: G 277 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8014 (tm-30) REVERT: G 319 ASP cc_start: 0.8192 (m-30) cc_final: 0.7886 (m-30) REVERT: G 327 SER cc_start: 0.8449 (p) cc_final: 0.8217 (p) REVERT: G 412 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7510 (ptt90) REVERT: G 474 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8466 (mtpt) REVERT: G 487 GLU cc_start: 0.8507 (tt0) cc_final: 0.8153 (tt0) REVERT: G 507 HIS cc_start: 0.8559 (t-90) cc_final: 0.8117 (t-90) REVERT: H 16 ASP cc_start: 0.8189 (t0) cc_final: 0.7932 (t0) REVERT: H 34 ASP cc_start: 0.8973 (t0) cc_final: 0.8695 (t0) REVERT: H 75 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: H 132 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8454 (pp20) REVERT: H 134 LYS cc_start: 0.7977 (pttp) cc_final: 0.7628 (pttm) REVERT: H 136 ARG cc_start: 0.8619 (ptm-80) cc_final: 0.8209 (ptt180) REVERT: H 179 MET cc_start: 0.7822 (pp-130) cc_final: 0.6736 (ppp) REVERT: H 194 LEU cc_start: 0.8842 (mm) cc_final: 0.8435 (mm) REVERT: H 198 ASN cc_start: 0.9300 (m-40) cc_final: 0.8798 (m-40) REVERT: H 214 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8282 (tm-30) REVERT: H 319 ASP cc_start: 0.8112 (m-30) cc_final: 0.7682 (m-30) REVERT: H 369 ASN cc_start: 0.8506 (p0) cc_final: 0.8260 (p0) REVERT: H 379 LEU cc_start: 0.9522 (mt) cc_final: 0.9311 (mt) REVERT: H 409 LYS cc_start: 0.8526 (ttmm) cc_final: 0.8196 (tppt) REVERT: H 412 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7595 (ptt90) REVERT: H 474 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8471 (mtpt) REVERT: H 507 HIS cc_start: 0.8519 (t-90) cc_final: 0.8076 (t-90) outliers start: 212 outliers final: 140 residues processed: 917 average time/residue: 0.4122 time to fit residues: 612.4102 Evaluate side-chains 905 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 744 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 379 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 0.0970 chunk 199 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32072 Z= 0.245 Angle : 0.670 8.872 43488 Z= 0.340 Chirality : 0.046 0.150 4968 Planarity : 0.004 0.041 5448 Dihedral : 13.147 77.198 5399 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 6.85 % Allowed : 23.56 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.91 (0.13), residues: 3968 helix: -0.46 (0.15), residues: 1280 sheet: -0.96 (0.24), residues: 464 loop : -1.87 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 253 PHE 0.012 0.001 PHE A 24 TYR 0.011 0.001 TYR A 400 ARG 0.005 0.000 ARG H 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 785 time to evaluate : 3.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8205 (t0) cc_final: 0.7977 (t0) REVERT: A 36 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8191 (pp) REVERT: A 75 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6208 (pm20) REVERT: A 134 LYS cc_start: 0.7962 (pttp) cc_final: 0.7712 (pttm) REVERT: A 136 ARG cc_start: 0.8541 (ptm-80) cc_final: 0.8068 (ptt90) REVERT: A 174 PHE cc_start: 0.8124 (m-80) cc_final: 0.7680 (t80) REVERT: A 179 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6336 (ppp) REVERT: A 203 ARG cc_start: 0.8810 (tpp-160) cc_final: 0.8270 (mtp-110) REVERT: A 214 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8162 (tm-30) REVERT: A 259 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8197 (mtp180) REVERT: A 319 ASP cc_start: 0.8210 (m-30) cc_final: 0.7815 (m-30) REVERT: A 327 SER cc_start: 0.8512 (p) cc_final: 0.8275 (p) REVERT: A 385 MET cc_start: 0.8519 (ttp) cc_final: 0.7984 (ttp) REVERT: A 409 LYS cc_start: 0.8327 (ttmm) cc_final: 0.8076 (tptt) REVERT: A 412 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7417 (ptt90) REVERT: A 474 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8467 (mtpt) REVERT: A 507 HIS cc_start: 0.8556 (t-90) cc_final: 0.8140 (t-90) REVERT: B 16 ASP cc_start: 0.8172 (t0) cc_final: 0.7921 (t0) REVERT: B 34 ASP cc_start: 0.8996 (t0) cc_final: 0.8692 (t0) REVERT: B 75 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6349 (pm20) REVERT: B 134 LYS cc_start: 0.8052 (pttp) cc_final: 0.7771 (pttm) REVERT: B 179 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6598 (ppp) REVERT: B 198 ASN cc_start: 0.9279 (m-40) cc_final: 0.8745 (m-40) REVERT: B 205 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8222 (ttmm) REVERT: B 214 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8309 (tm-30) REVERT: B 259 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8010 (mtp180) REVERT: B 319 ASP cc_start: 0.8153 (m-30) cc_final: 0.7778 (m-30) REVERT: B 379 LEU cc_start: 0.9499 (mt) cc_final: 0.9247 (mt) REVERT: B 412 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7483 (ptt90) REVERT: B 507 HIS cc_start: 0.8502 (t-90) cc_final: 0.8041 (t-90) REVERT: C 16 ASP cc_start: 0.8221 (t0) cc_final: 0.7986 (t0) REVERT: C 34 ASP cc_start: 0.8989 (t0) cc_final: 0.8637 (t0) REVERT: C 36 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8158 (pp) REVERT: C 75 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6252 (pm20) REVERT: C 134 LYS cc_start: 0.8034 (pttp) cc_final: 0.7770 (pttm) REVERT: C 136 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8070 (ptt90) REVERT: C 150 MET cc_start: 0.8039 (ttt) cc_final: 0.7810 (tpp) REVERT: C 174 PHE cc_start: 0.8192 (m-80) cc_final: 0.7789 (t80) REVERT: C 179 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6317 (ppp) REVERT: C 199 GLU cc_start: 0.8087 (pt0) cc_final: 0.7777 (tp30) REVERT: C 202 GLN cc_start: 0.8390 (pp30) cc_final: 0.8021 (pp30) REVERT: C 203 ARG cc_start: 0.8888 (tpp-160) cc_final: 0.8341 (mtp-110) REVERT: C 214 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8124 (tm-30) REVERT: C 352 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8328 (tm-30) REVERT: C 353 TYR cc_start: 0.8775 (t80) cc_final: 0.8524 (t80) REVERT: C 412 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7510 (ptt90) REVERT: C 474 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8479 (mtpt) REVERT: C 507 HIS cc_start: 0.8535 (t-90) cc_final: 0.8124 (t-90) REVERT: D 16 ASP cc_start: 0.8210 (t0) cc_final: 0.7946 (t0) REVERT: D 75 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6422 (pm20) REVERT: D 134 LYS cc_start: 0.7896 (pttp) cc_final: 0.7629 (pttm) REVERT: D 136 ARG cc_start: 0.8597 (ptm-80) cc_final: 0.8158 (ptt180) REVERT: D 150 MET cc_start: 0.8066 (ttt) cc_final: 0.7786 (tpp) REVERT: D 174 PHE cc_start: 0.8210 (m-80) cc_final: 0.7781 (t80) REVERT: D 179 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6607 (ppp) REVERT: D 205 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8227 (ttmm) REVERT: D 214 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8142 (tm-30) REVERT: D 319 ASP cc_start: 0.8218 (m-30) cc_final: 0.7782 (m-30) REVERT: D 412 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7565 (ptt90) REVERT: D 474 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8469 (mtpt) REVERT: D 507 HIS cc_start: 0.8551 (t-90) cc_final: 0.8135 (t-90) REVERT: E 16 ASP cc_start: 0.8079 (t0) cc_final: 0.7827 (t0) REVERT: E 34 ASP cc_start: 0.8959 (t0) cc_final: 0.8561 (t0) REVERT: E 65 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8733 (mm) REVERT: E 75 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6330 (pm20) REVERT: E 134 LYS cc_start: 0.8188 (pttp) cc_final: 0.7891 (pttm) REVERT: E 136 ARG cc_start: 0.8519 (ptm160) cc_final: 0.8175 (ptt180) REVERT: E 150 MET cc_start: 0.8019 (ttt) cc_final: 0.7540 (tpt) REVERT: E 179 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6466 (ppp) REVERT: E 198 ASN cc_start: 0.9296 (m-40) cc_final: 0.8764 (m-40) REVERT: E 199 GLU cc_start: 0.8041 (pt0) cc_final: 0.7672 (tp30) REVERT: E 202 GLN cc_start: 0.8530 (pp30) cc_final: 0.8113 (pp30) REVERT: E 203 ARG cc_start: 0.8794 (tpp-160) cc_final: 0.8139 (mtp-110) REVERT: E 214 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8147 (tm-30) REVERT: E 231 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7758 (mmm160) REVERT: E 245 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8140 (mm) REVERT: E 319 ASP cc_start: 0.8200 (m-30) cc_final: 0.7715 (m-30) REVERT: E 379 LEU cc_start: 0.9544 (mt) cc_final: 0.9284 (mt) REVERT: E 412 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7477 (ptt90) REVERT: E 474 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8456 (mtpt) REVERT: E 507 HIS cc_start: 0.8556 (t-90) cc_final: 0.8172 (t-90) REVERT: F 16 ASP cc_start: 0.8194 (t0) cc_final: 0.7941 (t0) REVERT: F 75 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6464 (pm20) REVERT: F 92 HIS cc_start: 0.8963 (p90) cc_final: 0.8678 (p-80) REVERT: F 134 LYS cc_start: 0.7872 (pttp) cc_final: 0.7531 (pttm) REVERT: F 136 ARG cc_start: 0.8639 (ptm-80) cc_final: 0.8320 (ptt180) REVERT: F 179 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6660 (ppp) REVERT: F 199 GLU cc_start: 0.8165 (pt0) cc_final: 0.7777 (tp30) REVERT: F 202 GLN cc_start: 0.8535 (pp30) cc_final: 0.8139 (pp30) REVERT: F 203 ARG cc_start: 0.8748 (tpp-160) cc_final: 0.8112 (mtp-110) REVERT: F 214 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8171 (tm-30) REVERT: F 286 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8515 (tmt) REVERT: F 319 ASP cc_start: 0.8162 (m-30) cc_final: 0.7684 (m-30) REVERT: F 412 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7620 (ptt90) REVERT: F 507 HIS cc_start: 0.8551 (t-90) cc_final: 0.8149 (t-90) REVERT: G 16 ASP cc_start: 0.8231 (t0) cc_final: 0.7996 (t0) REVERT: G 75 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6519 (pm20) REVERT: G 132 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8427 (pp20) REVERT: G 134 LYS cc_start: 0.8014 (pttp) cc_final: 0.7718 (pttm) REVERT: G 136 ARG cc_start: 0.8603 (ptm-80) cc_final: 0.8257 (ptt180) REVERT: G 174 PHE cc_start: 0.8114 (m-80) cc_final: 0.7679 (t80) REVERT: G 179 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6394 (ppp) REVERT: G 199 GLU cc_start: 0.8125 (pt0) cc_final: 0.7885 (tp30) REVERT: G 203 ARG cc_start: 0.8887 (tpp-160) cc_final: 0.8193 (mtp-110) REVERT: G 214 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8115 (tm-30) REVERT: G 231 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7843 (mmp80) REVERT: G 277 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8021 (tm-30) REVERT: G 319 ASP cc_start: 0.8209 (m-30) cc_final: 0.7872 (m-30) REVERT: G 412 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7471 (ptt90) REVERT: G 474 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8504 (mtpt) REVERT: G 487 GLU cc_start: 0.8491 (tt0) cc_final: 0.8058 (tt0) REVERT: G 507 HIS cc_start: 0.8566 (t-90) cc_final: 0.8131 (t-90) REVERT: H 16 ASP cc_start: 0.8206 (t0) cc_final: 0.7941 (t0) REVERT: H 34 ASP cc_start: 0.8996 (t0) cc_final: 0.8704 (t0) REVERT: H 65 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8402 (mm) REVERT: H 75 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6388 (pm20) REVERT: H 92 HIS cc_start: 0.8909 (p90) cc_final: 0.8656 (p-80) REVERT: H 132 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8470 (pp20) REVERT: H 134 LYS cc_start: 0.7978 (pttp) cc_final: 0.7684 (pttm) REVERT: H 136 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8168 (ptt180) REVERT: H 179 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6715 (ppp) REVERT: H 214 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8257 (tm-30) REVERT: H 319 ASP cc_start: 0.8151 (m-30) cc_final: 0.7728 (m-30) REVERT: H 379 LEU cc_start: 0.9528 (mt) cc_final: 0.9291 (mt) REVERT: H 409 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8197 (tppt) REVERT: H 412 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7581 (ptt90) REVERT: H 507 HIS cc_start: 0.8559 (t-90) cc_final: 0.8167 (t-90) outliers start: 224 outliers final: 153 residues processed: 894 average time/residue: 0.4034 time to fit residues: 584.4163 Evaluate side-chains 926 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 749 time to evaluate : 3.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 400 TYR Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 319 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 230 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32072 Z= 0.304 Angle : 0.704 8.965 43488 Z= 0.357 Chirality : 0.047 0.157 4968 Planarity : 0.004 0.039 5448 Dihedral : 13.157 80.065 5399 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 6.88 % Allowed : 24.45 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.91 (0.13), residues: 3968 helix: -0.42 (0.15), residues: 1280 sheet: -0.89 (0.25), residues: 464 loop : -1.92 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 92 PHE 0.013 0.001 PHE A 24 TYR 0.012 0.001 TYR E 348 ARG 0.007 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 752 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8202 (t0) cc_final: 0.7987 (t0) REVERT: A 36 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8341 (pp) REVERT: A 75 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: A 134 LYS cc_start: 0.7946 (pttp) cc_final: 0.7716 (pttm) REVERT: A 136 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.8128 (ptt90) REVERT: A 174 PHE cc_start: 0.8078 (m-80) cc_final: 0.7652 (t80) REVERT: A 179 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6632 (ppp) REVERT: A 203 ARG cc_start: 0.8745 (tpp-160) cc_final: 0.8254 (mtp-110) REVERT: A 214 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8196 (tm-30) REVERT: A 319 ASP cc_start: 0.8252 (m-30) cc_final: 0.7827 (m-30) REVERT: A 385 MET cc_start: 0.8612 (ttp) cc_final: 0.8071 (ttp) REVERT: A 412 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7454 (ptt90) REVERT: A 474 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8464 (mtpt) REVERT: A 507 HIS cc_start: 0.8539 (t-90) cc_final: 0.8119 (t-90) REVERT: B 16 ASP cc_start: 0.8153 (t0) cc_final: 0.7888 (t0) REVERT: B 75 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6329 (pm20) REVERT: B 134 LYS cc_start: 0.7982 (pttp) cc_final: 0.7723 (pttm) REVERT: B 179 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.6865 (ppp) REVERT: B 205 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8311 (ttmm) REVERT: B 214 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8313 (tm-30) REVERT: B 319 ASP cc_start: 0.8239 (m-30) cc_final: 0.7759 (m-30) REVERT: B 379 LEU cc_start: 0.9551 (mt) cc_final: 0.9305 (mt) REVERT: B 412 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7502 (ptt90) REVERT: B 507 HIS cc_start: 0.8542 (t-90) cc_final: 0.8109 (t-90) REVERT: C 34 ASP cc_start: 0.9061 (t0) cc_final: 0.8642 (t0) REVERT: C 36 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8271 (pp) REVERT: C 75 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6272 (pm20) REVERT: C 134 LYS cc_start: 0.8003 (pttp) cc_final: 0.7757 (pttm) REVERT: C 136 ARG cc_start: 0.8594 (ptm-80) cc_final: 0.8163 (ptt90) REVERT: C 150 MET cc_start: 0.8105 (ttt) cc_final: 0.7810 (tpp) REVERT: C 174 PHE cc_start: 0.8200 (m-80) cc_final: 0.7830 (t80) REVERT: C 179 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.6430 (ppp) REVERT: C 199 GLU cc_start: 0.8100 (pt0) cc_final: 0.7809 (tp30) REVERT: C 203 ARG cc_start: 0.8880 (tpp-160) cc_final: 0.8275 (mtp-110) REVERT: C 205 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8264 (ttmm) REVERT: C 214 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8158 (tm-30) REVERT: C 319 ASP cc_start: 0.8288 (m-30) cc_final: 0.7866 (m-30) REVERT: C 412 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7551 (ptt90) REVERT: C 474 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8467 (mtpt) REVERT: C 507 HIS cc_start: 0.8570 (t-90) cc_final: 0.8191 (t-90) REVERT: D 16 ASP cc_start: 0.8194 (t0) cc_final: 0.7962 (t0) REVERT: D 75 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6493 (pm20) REVERT: D 134 LYS cc_start: 0.7874 (pttp) cc_final: 0.7633 (pttm) REVERT: D 136 ARG cc_start: 0.8634 (ptm-80) cc_final: 0.8199 (ptt180) REVERT: D 150 MET cc_start: 0.8115 (ttt) cc_final: 0.7768 (tpp) REVERT: D 174 PHE cc_start: 0.8237 (m-80) cc_final: 0.7858 (t80) REVERT: D 179 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.6848 (ppp) REVERT: D 205 LYS cc_start: 0.8947 (mtpp) cc_final: 0.8189 (ttmm) REVERT: D 214 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8171 (tm-30) REVERT: D 412 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7515 (ptt90) REVERT: D 474 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8438 (mtpt) REVERT: D 507 HIS cc_start: 0.8559 (t-90) cc_final: 0.8140 (t-90) REVERT: E 16 ASP cc_start: 0.8113 (t0) cc_final: 0.7862 (t0) REVERT: E 34 ASP cc_start: 0.9041 (t0) cc_final: 0.8788 (t0) REVERT: E 75 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6421 (pm20) REVERT: E 134 LYS cc_start: 0.8116 (pttp) cc_final: 0.7864 (pttm) REVERT: E 136 ARG cc_start: 0.8598 (ptm160) cc_final: 0.8252 (ptt180) REVERT: E 150 MET cc_start: 0.8058 (ttt) cc_final: 0.7810 (ttt) REVERT: E 179 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6505 (ppp) REVERT: E 199 GLU cc_start: 0.8154 (pt0) cc_final: 0.7750 (tp30) REVERT: E 202 GLN cc_start: 0.8571 (pp30) cc_final: 0.8152 (pp30) REVERT: E 203 ARG cc_start: 0.8803 (tpp-160) cc_final: 0.8152 (mtp-110) REVERT: E 214 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8254 (tm-30) REVERT: E 231 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7747 (mmm160) REVERT: E 245 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8174 (mm) REVERT: E 319 ASP cc_start: 0.8330 (m-30) cc_final: 0.7758 (m-30) REVERT: E 412 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7510 (ptt90) REVERT: E 474 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8494 (mtpt) REVERT: E 507 HIS cc_start: 0.8535 (t-90) cc_final: 0.8127 (t-90) REVERT: F 75 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6449 (pm20) REVERT: F 134 LYS cc_start: 0.7906 (pttp) cc_final: 0.7565 (pttm) REVERT: F 136 ARG cc_start: 0.8709 (ptm-80) cc_final: 0.8358 (ptt180) REVERT: F 179 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.6860 (ppp) REVERT: F 199 GLU cc_start: 0.8166 (pt0) cc_final: 0.7789 (tp30) REVERT: F 202 GLN cc_start: 0.8544 (pp30) cc_final: 0.8144 (pp30) REVERT: F 203 ARG cc_start: 0.8743 (tpp-160) cc_final: 0.8122 (mtp-110) REVERT: F 214 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8179 (tm-30) REVERT: F 286 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8543 (tmt) REVERT: F 319 ASP cc_start: 0.8238 (m-30) cc_final: 0.7728 (m-30) REVERT: F 412 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7658 (ptt90) REVERT: F 507 HIS cc_start: 0.8556 (t-90) cc_final: 0.8146 (t-90) REVERT: G 16 ASP cc_start: 0.8183 (t0) cc_final: 0.7976 (t0) REVERT: G 75 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: G 132 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8468 (pp20) REVERT: G 134 LYS cc_start: 0.8026 (pttp) cc_final: 0.7767 (pttm) REVERT: G 136 ARG cc_start: 0.8650 (ptm-80) cc_final: 0.8185 (ptt180) REVERT: G 174 PHE cc_start: 0.8036 (m-80) cc_final: 0.7463 (t80) REVERT: G 179 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.6612 (ppp) REVERT: G 199 GLU cc_start: 0.8149 (pt0) cc_final: 0.7831 (tp30) REVERT: G 202 GLN cc_start: 0.8281 (pp30) cc_final: 0.7719 (pp30) REVERT: G 203 ARG cc_start: 0.8875 (tpp-160) cc_final: 0.8239 (mtp-110) REVERT: G 214 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8183 (tm-30) REVERT: G 319 ASP cc_start: 0.8253 (m-30) cc_final: 0.7807 (m-30) REVERT: G 412 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7547 (ptt90) REVERT: G 474 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8489 (mtpt) REVERT: G 487 GLU cc_start: 0.8516 (tt0) cc_final: 0.8085 (tt0) REVERT: G 507 HIS cc_start: 0.8547 (t-90) cc_final: 0.8125 (t-90) REVERT: H 16 ASP cc_start: 0.8203 (t0) cc_final: 0.7973 (t0) REVERT: H 36 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8352 (pp) REVERT: H 65 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8444 (mm) REVERT: H 75 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6361 (pm20) REVERT: H 92 HIS cc_start: 0.8964 (p90) cc_final: 0.8696 (p-80) REVERT: H 132 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8467 (pp20) REVERT: H 134 LYS cc_start: 0.8013 (pttp) cc_final: 0.7749 (pttm) REVERT: H 136 ARG cc_start: 0.8704 (ptm-80) cc_final: 0.8186 (ptt180) REVERT: H 179 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.6890 (ppp) REVERT: H 214 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8257 (tm-30) REVERT: H 319 ASP cc_start: 0.8288 (m-30) cc_final: 0.7763 (m-30) REVERT: H 379 LEU cc_start: 0.9550 (mt) cc_final: 0.9300 (mt) REVERT: H 409 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8247 (tppt) REVERT: H 412 ARG cc_start: 0.8109 (ttp80) cc_final: 0.7579 (ptt90) REVERT: H 507 HIS cc_start: 0.8584 (t-90) cc_final: 0.8193 (t-90) outliers start: 225 outliers final: 161 residues processed: 873 average time/residue: 0.4220 time to fit residues: 603.6209 Evaluate side-chains 911 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 726 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 257 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 296 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32072 Z= 0.233 Angle : 0.682 9.015 43488 Z= 0.344 Chirality : 0.046 0.150 4968 Planarity : 0.004 0.037 5448 Dihedral : 12.794 81.672 5399 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 6.08 % Allowed : 25.52 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.76 (0.13), residues: 3968 helix: -0.27 (0.15), residues: 1264 sheet: -0.76 (0.25), residues: 464 loop : -1.85 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS D 92 PHE 0.010 0.001 PHE A 24 TYR 0.019 0.001 TYR C 289 ARG 0.005 0.000 ARG G 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 786 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8147 (t0) cc_final: 0.7926 (t0) REVERT: A 36 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8269 (pp) REVERT: A 75 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: A 82 MET cc_start: 0.8786 (tpp) cc_final: 0.8580 (tpp) REVERT: A 134 LYS cc_start: 0.8058 (pttp) cc_final: 0.7836 (pttm) REVERT: A 136 ARG cc_start: 0.8575 (ptm-80) cc_final: 0.8150 (ptt90) REVERT: A 174 PHE cc_start: 0.8079 (m-80) cc_final: 0.7652 (t80) REVERT: A 179 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.6679 (ppp) REVERT: A 203 ARG cc_start: 0.8829 (tpp-160) cc_final: 0.8316 (mtp-110) REVERT: A 214 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8190 (tm-30) REVERT: A 319 ASP cc_start: 0.8233 (m-30) cc_final: 0.7811 (m-30) REVERT: A 385 MET cc_start: 0.8654 (ttp) cc_final: 0.8123 (ttp) REVERT: A 412 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7307 (ptt90) REVERT: A 441 GLN cc_start: 0.8768 (tt0) cc_final: 0.8469 (mt0) REVERT: A 474 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8541 (mtpt) REVERT: A 507 HIS cc_start: 0.8529 (t-90) cc_final: 0.8113 (t-90) REVERT: B 16 ASP cc_start: 0.8153 (t0) cc_final: 0.7914 (t0) REVERT: B 75 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6272 (pm20) REVERT: B 134 LYS cc_start: 0.7965 (pttp) cc_final: 0.7720 (pttm) REVERT: B 179 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.6836 (ppp) REVERT: B 202 GLN cc_start: 0.8319 (pp30) cc_final: 0.7874 (pp30) REVERT: B 205 LYS cc_start: 0.8993 (mtpp) cc_final: 0.8405 (ttmm) REVERT: B 209 LEU cc_start: 0.8248 (tt) cc_final: 0.7996 (tt) REVERT: B 214 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8324 (tm-30) REVERT: B 259 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8267 (mtp180) REVERT: B 319 ASP cc_start: 0.8220 (m-30) cc_final: 0.7705 (m-30) REVERT: B 360 PRO cc_start: 0.9385 (Cg_exo) cc_final: 0.9183 (Cg_endo) REVERT: B 379 LEU cc_start: 0.9524 (mt) cc_final: 0.9257 (mt) REVERT: B 412 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7451 (ptt90) REVERT: B 507 HIS cc_start: 0.8540 (t-90) cc_final: 0.8134 (t-90) REVERT: C 34 ASP cc_start: 0.8963 (t0) cc_final: 0.8645 (t0) REVERT: C 36 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8211 (pp) REVERT: C 63 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8764 (t) REVERT: C 75 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6260 (pm20) REVERT: C 82 MET cc_start: 0.8819 (tpp) cc_final: 0.8608 (tpp) REVERT: C 128 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6617 (mtt90) REVERT: C 134 LYS cc_start: 0.8088 (pttp) cc_final: 0.7866 (pttm) REVERT: C 136 ARG cc_start: 0.8571 (ptm-80) cc_final: 0.8154 (ptt90) REVERT: C 150 MET cc_start: 0.8093 (ttt) cc_final: 0.7832 (tpp) REVERT: C 174 PHE cc_start: 0.8212 (m-80) cc_final: 0.7822 (t80) REVERT: C 179 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.6606 (ppp) REVERT: C 199 GLU cc_start: 0.8109 (pt0) cc_final: 0.7833 (tp30) REVERT: C 202 GLN cc_start: 0.8585 (pp30) cc_final: 0.8316 (pp30) REVERT: C 203 ARG cc_start: 0.8915 (tpp-160) cc_final: 0.8349 (ttp-110) REVERT: C 205 LYS cc_start: 0.8932 (mtpp) cc_final: 0.8283 (ttmm) REVERT: C 214 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8157 (tm-30) REVERT: C 319 ASP cc_start: 0.8281 (m-30) cc_final: 0.7867 (m-30) REVERT: C 379 LEU cc_start: 0.9499 (mt) cc_final: 0.9264 (mt) REVERT: C 412 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7462 (ptt90) REVERT: C 474 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8324 (mtpt) REVERT: C 507 HIS cc_start: 0.8560 (t-90) cc_final: 0.8200 (t-90) REVERT: D 16 ASP cc_start: 0.8115 (t0) cc_final: 0.7873 (t0) REVERT: D 75 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6321 (pm20) REVERT: D 134 LYS cc_start: 0.7855 (pttp) cc_final: 0.7642 (pttm) REVERT: D 136 ARG cc_start: 0.8623 (ptm-80) cc_final: 0.8282 (ptt180) REVERT: D 150 MET cc_start: 0.8133 (ttt) cc_final: 0.7832 (tpp) REVERT: D 174 PHE cc_start: 0.8271 (m-80) cc_final: 0.7965 (t80) REVERT: D 179 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.6858 (ppp) REVERT: D 205 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8161 (ttmm) REVERT: D 214 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8260 (tm-30) REVERT: D 245 LEU cc_start: 0.8279 (mm) cc_final: 0.8004 (mm) REVERT: D 412 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7402 (ptt90) REVERT: D 474 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8538 (mtpt) REVERT: D 507 HIS cc_start: 0.8541 (t-90) cc_final: 0.8156 (t-90) REVERT: E 16 ASP cc_start: 0.8060 (t0) cc_final: 0.7804 (t0) REVERT: E 34 ASP cc_start: 0.8972 (t0) cc_final: 0.8552 (t0) REVERT: E 75 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6314 (pm20) REVERT: E 92 HIS cc_start: 0.8987 (p90) cc_final: 0.8773 (p-80) REVERT: E 134 LYS cc_start: 0.8085 (pttp) cc_final: 0.7825 (pttm) REVERT: E 136 ARG cc_start: 0.8529 (ptm160) cc_final: 0.8224 (ptt180) REVERT: E 150 MET cc_start: 0.8003 (ttt) cc_final: 0.7749 (tpp) REVERT: E 179 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.6584 (ppp) REVERT: E 198 ASN cc_start: 0.9280 (m-40) cc_final: 0.8701 (m-40) REVERT: E 199 GLU cc_start: 0.8048 (pt0) cc_final: 0.7693 (tp30) REVERT: E 202 GLN cc_start: 0.8614 (pp30) cc_final: 0.8195 (pp30) REVERT: E 203 ARG cc_start: 0.8806 (tpp-160) cc_final: 0.8142 (mtp-110) REVERT: E 214 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8261 (tm-30) REVERT: E 231 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7674 (mmm160) REVERT: E 245 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8192 (mm) REVERT: E 319 ASP cc_start: 0.8247 (m-30) cc_final: 0.7704 (m-30) REVERT: E 379 LEU cc_start: 0.9549 (mt) cc_final: 0.9262 (mt) REVERT: E 412 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7440 (ptt90) REVERT: E 507 HIS cc_start: 0.8519 (t-90) cc_final: 0.8102 (t-90) REVERT: F 16 ASP cc_start: 0.8175 (t0) cc_final: 0.7930 (t0) REVERT: F 75 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6452 (pm20) REVERT: F 134 LYS cc_start: 0.7893 (pttp) cc_final: 0.7515 (tptt) REVERT: F 136 ARG cc_start: 0.8669 (ptm-80) cc_final: 0.8362 (ptt180) REVERT: F 179 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.6872 (ppp) REVERT: F 199 GLU cc_start: 0.8216 (pt0) cc_final: 0.7784 (tp30) REVERT: F 202 GLN cc_start: 0.8589 (pp30) cc_final: 0.8162 (pp30) REVERT: F 203 ARG cc_start: 0.8746 (tpp-160) cc_final: 0.8071 (mtp-110) REVERT: F 214 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8180 (tm-30) REVERT: F 319 ASP cc_start: 0.8272 (m-30) cc_final: 0.7797 (m-30) REVERT: F 379 LEU cc_start: 0.9456 (mt) cc_final: 0.9221 (mt) REVERT: F 412 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7591 (ptt90) REVERT: F 507 HIS cc_start: 0.8542 (t-90) cc_final: 0.8142 (t-90) REVERT: G 16 ASP cc_start: 0.8182 (t0) cc_final: 0.7977 (t0) REVERT: G 63 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8765 (t) REVERT: G 75 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6489 (pm20) REVERT: G 92 HIS cc_start: 0.8997 (p90) cc_final: 0.8787 (p-80) REVERT: G 132 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8489 (pp20) REVERT: G 134 LYS cc_start: 0.8044 (pttp) cc_final: 0.7786 (pttm) REVERT: G 136 ARG cc_start: 0.8624 (ptm-80) cc_final: 0.8224 (ptt180) REVERT: G 174 PHE cc_start: 0.8053 (m-80) cc_final: 0.7482 (t80) REVERT: G 179 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6568 (ppp) REVERT: G 199 GLU cc_start: 0.8157 (pt0) cc_final: 0.7854 (tp30) REVERT: G 202 GLN cc_start: 0.8395 (pp30) cc_final: 0.7852 (pp30) REVERT: G 203 ARG cc_start: 0.8904 (tpp-160) cc_final: 0.8284 (mtp-110) REVERT: G 214 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8216 (tm-30) REVERT: G 319 ASP cc_start: 0.8230 (m-30) cc_final: 0.7930 (m-30) REVERT: G 379 LEU cc_start: 0.9521 (mt) cc_final: 0.9246 (mt) REVERT: G 412 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7376 (ptt90) REVERT: G 474 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8531 (mtpt) REVERT: G 487 GLU cc_start: 0.8499 (tt0) cc_final: 0.8067 (tt0) REVERT: G 507 HIS cc_start: 0.8547 (t-90) cc_final: 0.8134 (t-90) REVERT: H 16 ASP cc_start: 0.8183 (t0) cc_final: 0.7953 (t0) REVERT: H 65 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8394 (mm) REVERT: H 75 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6358 (pm20) REVERT: H 92 HIS cc_start: 0.8930 (p90) cc_final: 0.8676 (p-80) REVERT: H 134 LYS cc_start: 0.7972 (pttp) cc_final: 0.7712 (pttm) REVERT: H 179 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6978 (ppp) REVERT: H 214 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8290 (tm-30) REVERT: H 319 ASP cc_start: 0.8200 (m-30) cc_final: 0.7718 (m-30) REVERT: H 379 LEU cc_start: 0.9527 (mt) cc_final: 0.9268 (mt) REVERT: H 412 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7575 (ptt90) REVERT: H 448 GLN cc_start: 0.8289 (pt0) cc_final: 0.8087 (pt0) REVERT: H 507 HIS cc_start: 0.8568 (t-90) cc_final: 0.8208 (t-90) outliers start: 199 outliers final: 151 residues processed: 885 average time/residue: 0.4041 time to fit residues: 587.2323 Evaluate side-chains 929 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 754 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 7.9990 chunk 361 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 352 optimal weight: 0.6980 chunk 211 optimal weight: 0.0980 chunk 153 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 350 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32072 Z= 0.250 Angle : 0.689 8.379 43488 Z= 0.348 Chirality : 0.046 0.139 4968 Planarity : 0.004 0.036 5448 Dihedral : 12.626 84.077 5399 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 5.90 % Allowed : 26.28 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.13), residues: 3968 helix: -0.25 (0.15), residues: 1256 sheet: -0.74 (0.25), residues: 464 loop : -1.83 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 92 PHE 0.010 0.001 PHE D 401 TYR 0.016 0.001 TYR E 233 ARG 0.004 0.000 ARG H 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 773 time to evaluate : 4.189 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8132 (t0) cc_final: 0.7919 (t0) REVERT: A 36 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8265 (pp) REVERT: A 75 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6309 (pm20) REVERT: A 128 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6581 (mtt90) REVERT: A 136 ARG cc_start: 0.8580 (ptm-80) cc_final: 0.8178 (ptt90) REVERT: A 174 PHE cc_start: 0.8071 (m-80) cc_final: 0.7638 (t80) REVERT: A 179 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6669 (ppp) REVERT: A 198 ASN cc_start: 0.9353 (m-40) cc_final: 0.8751 (m-40) REVERT: A 203 ARG cc_start: 0.8830 (tpp-160) cc_final: 0.8318 (mtp-110) REVERT: A 214 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8281 (tm-30) REVERT: A 319 ASP cc_start: 0.8219 (m-30) cc_final: 0.7813 (m-30) REVERT: A 385 MET cc_start: 0.8698 (ttp) cc_final: 0.8168 (ttp) REVERT: A 412 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7293 (ptt90) REVERT: A 474 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8488 (mtpt) REVERT: A 507 HIS cc_start: 0.8541 (t-90) cc_final: 0.8153 (t-90) REVERT: B 16 ASP cc_start: 0.8068 (t0) cc_final: 0.7835 (t0) REVERT: B 75 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6392 (pm20) REVERT: B 134 LYS cc_start: 0.8055 (pttp) cc_final: 0.7812 (pttm) REVERT: B 179 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6853 (ppp) REVERT: B 198 ASN cc_start: 0.9300 (m-40) cc_final: 0.8817 (m-40) REVERT: B 202 GLN cc_start: 0.8392 (pp30) cc_final: 0.7955 (pp30) REVERT: B 205 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8387 (ttmm) REVERT: B 209 LEU cc_start: 0.8279 (tt) cc_final: 0.8032 (tt) REVERT: B 214 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8379 (tm-30) REVERT: B 259 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8298 (mtp180) REVERT: B 319 ASP cc_start: 0.8223 (m-30) cc_final: 0.7682 (m-30) REVERT: B 360 PRO cc_start: 0.9393 (Cg_exo) cc_final: 0.9189 (Cg_endo) REVERT: B 379 LEU cc_start: 0.9518 (mt) cc_final: 0.9276 (mt) REVERT: B 412 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7460 (ptt90) REVERT: B 507 HIS cc_start: 0.8553 (t-90) cc_final: 0.8166 (t-90) REVERT: C 34 ASP cc_start: 0.8988 (t0) cc_final: 0.8653 (t0) REVERT: C 36 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8174 (pp) REVERT: C 75 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: C 82 MET cc_start: 0.8781 (tpp) cc_final: 0.8577 (tpp) REVERT: C 128 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6568 (mtt90) REVERT: C 134 LYS cc_start: 0.8113 (pttp) cc_final: 0.7888 (pttm) REVERT: C 136 ARG cc_start: 0.8586 (ptm-80) cc_final: 0.8178 (ptt90) REVERT: C 150 MET cc_start: 0.8066 (ttt) cc_final: 0.7800 (tpp) REVERT: C 174 PHE cc_start: 0.8202 (m-80) cc_final: 0.7829 (t80) REVERT: C 179 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6618 (ppp) REVERT: C 198 ASN cc_start: 0.9300 (m-40) cc_final: 0.8725 (m-40) REVERT: C 199 GLU cc_start: 0.8101 (pt0) cc_final: 0.7826 (tp30) REVERT: C 202 GLN cc_start: 0.8525 (pp30) cc_final: 0.8191 (pp30) REVERT: C 203 ARG cc_start: 0.8899 (tpp-160) cc_final: 0.8225 (mtp-110) REVERT: C 205 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8218 (ttmm) REVERT: C 214 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8252 (tm-30) REVERT: C 319 ASP cc_start: 0.8279 (m-30) cc_final: 0.7853 (m-30) REVERT: C 379 LEU cc_start: 0.9464 (mt) cc_final: 0.9134 (mt) REVERT: C 412 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7444 (ptt90) REVERT: C 474 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8347 (mtpt) REVERT: C 483 MET cc_start: 0.9121 (tmm) cc_final: 0.8487 (tmm) REVERT: C 507 HIS cc_start: 0.8582 (t-90) cc_final: 0.8224 (t-90) REVERT: D 16 ASP cc_start: 0.8147 (t0) cc_final: 0.7928 (t0) REVERT: D 75 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6278 (pm20) REVERT: D 109 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7111 (ptpt) REVERT: D 136 ARG cc_start: 0.8620 (ptm-80) cc_final: 0.8278 (ptt180) REVERT: D 150 MET cc_start: 0.8129 (ttt) cc_final: 0.7807 (tpp) REVERT: D 174 PHE cc_start: 0.8270 (m-80) cc_final: 0.7984 (t80) REVERT: D 179 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6821 (ppp) REVERT: D 205 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8229 (ttmm) REVERT: D 214 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8239 (tm-30) REVERT: D 245 LEU cc_start: 0.8174 (mm) cc_final: 0.7955 (mm) REVERT: D 412 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7459 (ptt90) REVERT: D 474 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8560 (mtpt) REVERT: D 507 HIS cc_start: 0.8555 (t-90) cc_final: 0.8178 (t-90) REVERT: E 16 ASP cc_start: 0.8050 (t0) cc_final: 0.7766 (t0) REVERT: E 34 ASP cc_start: 0.8943 (t0) cc_final: 0.8584 (t0) REVERT: E 75 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6307 (pm20) REVERT: E 92 HIS cc_start: 0.9001 (p90) cc_final: 0.8778 (p-80) REVERT: E 134 LYS cc_start: 0.8059 (pttp) cc_final: 0.7813 (pttm) REVERT: E 136 ARG cc_start: 0.8574 (ptm160) cc_final: 0.8261 (ptt180) REVERT: E 150 MET cc_start: 0.8066 (ttt) cc_final: 0.7821 (ttt) REVERT: E 179 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6597 (ppp) REVERT: E 198 ASN cc_start: 0.9302 (m-40) cc_final: 0.8697 (m-40) REVERT: E 199 GLU cc_start: 0.8063 (pt0) cc_final: 0.7455 (tp30) REVERT: E 202 GLN cc_start: 0.8622 (pp30) cc_final: 0.7924 (pp30) REVERT: E 203 ARG cc_start: 0.8828 (tpp-160) cc_final: 0.8086 (mtp-110) REVERT: E 214 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8251 (tm-30) REVERT: E 231 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7747 (mmm160) REVERT: E 319 ASP cc_start: 0.8235 (m-30) cc_final: 0.7696 (m-30) REVERT: E 379 LEU cc_start: 0.9555 (mt) cc_final: 0.9275 (mt) REVERT: E 412 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7444 (ptt90) REVERT: E 507 HIS cc_start: 0.8549 (t-90) cc_final: 0.8146 (t-90) REVERT: F 16 ASP cc_start: 0.8120 (t0) cc_final: 0.7882 (t0) REVERT: F 70 MET cc_start: 0.9060 (ptt) cc_final: 0.8757 (ptt) REVERT: F 75 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6417 (pm20) REVERT: F 134 LYS cc_start: 0.7892 (pttp) cc_final: 0.7522 (tptt) REVERT: F 136 ARG cc_start: 0.8674 (ptm-80) cc_final: 0.8372 (ptt180) REVERT: F 179 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.6896 (ppp) REVERT: F 199 GLU cc_start: 0.8111 (pt0) cc_final: 0.7405 (tp30) REVERT: F 202 GLN cc_start: 0.8562 (pp30) cc_final: 0.7826 (pp30) REVERT: F 203 ARG cc_start: 0.8749 (tpp-160) cc_final: 0.8018 (mtp-110) REVERT: F 214 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8246 (tm-30) REVERT: F 230 ASN cc_start: 0.8902 (t0) cc_final: 0.8610 (t0) REVERT: F 319 ASP cc_start: 0.8256 (m-30) cc_final: 0.7770 (m-30) REVERT: F 412 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7553 (ptt90) REVERT: F 483 MET cc_start: 0.9081 (tmm) cc_final: 0.8391 (tmm) REVERT: F 507 HIS cc_start: 0.8527 (t-90) cc_final: 0.8162 (t-90) REVERT: G 16 ASP cc_start: 0.8171 (t0) cc_final: 0.7877 (t0) REVERT: G 75 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6533 (pm20) REVERT: G 92 HIS cc_start: 0.8998 (p90) cc_final: 0.8775 (p-80) REVERT: G 129 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6261 (p0) REVERT: G 132 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8495 (pp20) REVERT: G 134 LYS cc_start: 0.8076 (pttp) cc_final: 0.7855 (pttm) REVERT: G 136 ARG cc_start: 0.8634 (ptm-80) cc_final: 0.8234 (ptt180) REVERT: G 174 PHE cc_start: 0.8104 (m-80) cc_final: 0.7505 (t80) REVERT: G 179 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.6593 (ppp) REVERT: G 198 ASN cc_start: 0.9313 (m-40) cc_final: 0.8740 (m-40) REVERT: G 199 GLU cc_start: 0.8064 (pt0) cc_final: 0.7798 (tp30) REVERT: G 203 ARG cc_start: 0.8896 (tpp-160) cc_final: 0.8226 (mtp-110) REVERT: G 214 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8230 (tm-30) REVERT: G 273 LEU cc_start: 0.8722 (mt) cc_final: 0.8476 (mt) REVERT: G 319 ASP cc_start: 0.8256 (m-30) cc_final: 0.7946 (m-30) REVERT: G 412 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7385 (ptt90) REVERT: G 474 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8542 (mtpt) REVERT: G 483 MET cc_start: 0.9179 (tmm) cc_final: 0.8664 (tmm) REVERT: G 507 HIS cc_start: 0.8548 (t-90) cc_final: 0.8138 (t-90) REVERT: H 16 ASP cc_start: 0.8139 (t0) cc_final: 0.7898 (t0) REVERT: H 65 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8387 (mm) REVERT: H 75 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: H 92 HIS cc_start: 0.8925 (p90) cc_final: 0.8656 (p-80) REVERT: H 134 LYS cc_start: 0.7997 (pttp) cc_final: 0.7761 (pttm) REVERT: H 179 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7000 (ppp) REVERT: H 214 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8330 (tm-30) REVERT: H 319 ASP cc_start: 0.8199 (m-30) cc_final: 0.7706 (m-30) REVERT: H 412 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7589 (ptt90) REVERT: H 507 HIS cc_start: 0.8571 (t-90) cc_final: 0.8205 (t-90) outliers start: 193 outliers final: 145 residues processed: 871 average time/residue: 0.4057 time to fit residues: 576.3112 Evaluate side-chains 915 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 746 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.9980 chunk 372 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 390 optimal weight: 2.9990 chunk 359 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 240 optimal weight: 0.6980 chunk 190 optimal weight: 0.0170 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 HIS ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32072 Z= 0.226 Angle : 0.693 9.518 43488 Z= 0.347 Chirality : 0.046 0.154 4968 Planarity : 0.004 0.036 5448 Dihedral : 12.423 84.903 5399 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 5.20 % Allowed : 27.20 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.60 (0.13), residues: 3968 helix: -0.22 (0.15), residues: 1256 sheet: -0.76 (0.26), residues: 424 loop : -1.66 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS C 92 PHE 0.009 0.001 PHE A 24 TYR 0.018 0.001 TYR E 233 ARG 0.007 0.000 ARG H 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 779 time to evaluate : 3.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8101 (t0) cc_final: 0.7895 (t0) REVERT: A 36 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8234 (pp) REVERT: A 75 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6297 (mp0) REVERT: A 136 ARG cc_start: 0.8548 (ptm-80) cc_final: 0.8119 (ptt90) REVERT: A 174 PHE cc_start: 0.8076 (m-80) cc_final: 0.7636 (t80) REVERT: A 179 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6657 (ppp) REVERT: A 198 ASN cc_start: 0.9357 (m-40) cc_final: 0.8774 (m-40) REVERT: A 203 ARG cc_start: 0.8830 (tpp-160) cc_final: 0.8317 (mtp-110) REVERT: A 214 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8291 (tm-30) REVERT: A 319 ASP cc_start: 0.8239 (m-30) cc_final: 0.7818 (m-30) REVERT: A 385 MET cc_start: 0.8676 (ttp) cc_final: 0.8163 (ttp) REVERT: A 409 LYS cc_start: 0.8193 (tptt) cc_final: 0.7933 (tptt) REVERT: A 412 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7235 (ptt90) REVERT: A 441 GLN cc_start: 0.8776 (tt0) cc_final: 0.8464 (mt0) REVERT: A 507 HIS cc_start: 0.8548 (t-90) cc_final: 0.8172 (t-90) REVERT: B 16 ASP cc_start: 0.8133 (t0) cc_final: 0.7905 (t0) REVERT: B 75 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6366 (pm20) REVERT: B 134 LYS cc_start: 0.8047 (pttp) cc_final: 0.7826 (pttm) REVERT: B 136 ARG cc_start: 0.8596 (ptm160) cc_final: 0.8201 (ptt180) REVERT: B 179 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.6831 (ppp) REVERT: B 198 ASN cc_start: 0.9308 (m-40) cc_final: 0.8786 (m-40) REVERT: B 202 GLN cc_start: 0.8464 (pp30) cc_final: 0.8058 (pp30) REVERT: B 205 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8461 (ttmm) REVERT: B 209 LEU cc_start: 0.8297 (tt) cc_final: 0.8062 (tt) REVERT: B 214 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8375 (tm-30) REVERT: B 259 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8276 (mtp180) REVERT: B 319 ASP cc_start: 0.8209 (m-30) cc_final: 0.7696 (m-30) REVERT: B 360 PRO cc_start: 0.9355 (Cg_exo) cc_final: 0.9147 (Cg_endo) REVERT: B 412 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7432 (ptt90) REVERT: B 507 HIS cc_start: 0.8533 (t-90) cc_final: 0.8148 (t-90) REVERT: C 34 ASP cc_start: 0.8942 (t0) cc_final: 0.8623 (t0) REVERT: C 36 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8190 (pp) REVERT: C 75 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: C 82 MET cc_start: 0.8763 (tpp) cc_final: 0.8562 (tpp) REVERT: C 128 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6571 (mtt90) REVERT: C 134 LYS cc_start: 0.8090 (pttp) cc_final: 0.7887 (pttm) REVERT: C 136 ARG cc_start: 0.8568 (ptm-80) cc_final: 0.8129 (ptt90) REVERT: C 150 MET cc_start: 0.8052 (ttt) cc_final: 0.7792 (tpp) REVERT: C 174 PHE cc_start: 0.8201 (m-80) cc_final: 0.7812 (t80) REVERT: C 179 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6560 (ppp) REVERT: C 198 ASN cc_start: 0.9304 (m-40) cc_final: 0.8732 (m-40) REVERT: C 199 GLU cc_start: 0.8054 (pt0) cc_final: 0.7748 (tp30) REVERT: C 202 GLN cc_start: 0.8605 (pp30) cc_final: 0.8288 (pp30) REVERT: C 203 ARG cc_start: 0.8901 (tpp-160) cc_final: 0.8227 (mtp-110) REVERT: C 205 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8226 (ttmm) REVERT: C 214 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8261 (tm-30) REVERT: C 319 ASP cc_start: 0.8271 (m-30) cc_final: 0.7837 (m-30) REVERT: C 379 LEU cc_start: 0.9463 (mt) cc_final: 0.9139 (mt) REVERT: C 412 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7468 (ptt90) REVERT: C 474 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8284 (mtpt) REVERT: C 483 MET cc_start: 0.9132 (tmm) cc_final: 0.8531 (tmm) REVERT: C 507 HIS cc_start: 0.8576 (t-90) cc_final: 0.8223 (t-90) REVERT: D 16 ASP cc_start: 0.8111 (t0) cc_final: 0.7895 (t0) REVERT: D 75 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6247 (pm20) REVERT: D 136 ARG cc_start: 0.8616 (ptm-80) cc_final: 0.8276 (ptt180) REVERT: D 150 MET cc_start: 0.8036 (ttt) cc_final: 0.7805 (tpp) REVERT: D 174 PHE cc_start: 0.8276 (m-80) cc_final: 0.7993 (t80) REVERT: D 179 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.6898 (ppp) REVERT: D 205 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8221 (ttmm) REVERT: D 214 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8247 (tm-30) REVERT: D 412 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7423 (ptt90) REVERT: D 474 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8576 (mtpt) REVERT: D 483 MET cc_start: 0.9161 (tmm) cc_final: 0.8560 (tmm) REVERT: D 507 HIS cc_start: 0.8541 (t-90) cc_final: 0.8170 (t-90) REVERT: E 16 ASP cc_start: 0.8018 (t0) cc_final: 0.7780 (t0) REVERT: E 34 ASP cc_start: 0.8931 (t0) cc_final: 0.8545 (t0) REVERT: E 75 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6344 (pm20) REVERT: E 92 HIS cc_start: 0.9007 (p90) cc_final: 0.8788 (p-80) REVERT: E 134 LYS cc_start: 0.8086 (pttp) cc_final: 0.7849 (pttm) REVERT: E 136 ARG cc_start: 0.8565 (ptm160) cc_final: 0.8256 (ptt180) REVERT: E 150 MET cc_start: 0.8052 (ttt) cc_final: 0.7831 (tpp) REVERT: E 179 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.6694 (ppp) REVERT: E 198 ASN cc_start: 0.9299 (m-40) cc_final: 0.8684 (m-40) REVERT: E 199 GLU cc_start: 0.8056 (pt0) cc_final: 0.7454 (tp30) REVERT: E 202 GLN cc_start: 0.8633 (pp30) cc_final: 0.7931 (pp30) REVERT: E 203 ARG cc_start: 0.8821 (tpp-160) cc_final: 0.8066 (mtp-110) REVERT: E 214 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8261 (tm-30) REVERT: E 231 ARG cc_start: 0.8038 (mmm160) cc_final: 0.7714 (mmm160) REVERT: E 232 ASP cc_start: 0.8123 (t0) cc_final: 0.7903 (t0) REVERT: E 319 ASP cc_start: 0.8228 (m-30) cc_final: 0.7708 (m-30) REVERT: E 379 LEU cc_start: 0.9531 (mt) cc_final: 0.9246 (mt) REVERT: E 412 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7387 (ptt90) REVERT: E 507 HIS cc_start: 0.8499 (t-90) cc_final: 0.8135 (t-90) REVERT: F 16 ASP cc_start: 0.8088 (t0) cc_final: 0.7878 (t0) REVERT: F 70 MET cc_start: 0.9064 (ptt) cc_final: 0.8791 (ptt) REVERT: F 75 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6301 (pm20) REVERT: F 134 LYS cc_start: 0.7889 (pttp) cc_final: 0.7536 (tptt) REVERT: F 136 ARG cc_start: 0.8667 (ptm-80) cc_final: 0.8372 (ptt180) REVERT: F 179 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.6881 (ppp) REVERT: F 199 GLU cc_start: 0.8138 (pt0) cc_final: 0.7493 (tp30) REVERT: F 202 GLN cc_start: 0.8602 (pp30) cc_final: 0.7924 (pp30) REVERT: F 203 ARG cc_start: 0.8757 (tpp-160) cc_final: 0.8084 (ttp-110) REVERT: F 214 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8247 (tm-30) REVERT: F 319 ASP cc_start: 0.8212 (m-30) cc_final: 0.7748 (m-30) REVERT: F 412 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7533 (ptt90) REVERT: F 483 MET cc_start: 0.9086 (tmm) cc_final: 0.8501 (tmm) REVERT: F 507 HIS cc_start: 0.8530 (t-90) cc_final: 0.8157 (t-90) REVERT: G 16 ASP cc_start: 0.8132 (t0) cc_final: 0.7842 (t0) REVERT: G 63 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8661 (t) REVERT: G 75 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6441 (pm20) REVERT: G 92 HIS cc_start: 0.8967 (p90) cc_final: 0.8747 (p-80) REVERT: G 129 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.6438 (p0) REVERT: G 134 LYS cc_start: 0.8060 (pttp) cc_final: 0.7853 (pttm) REVERT: G 174 PHE cc_start: 0.8103 (m-80) cc_final: 0.7493 (t80) REVERT: G 179 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6590 (ppp) REVERT: G 198 ASN cc_start: 0.9302 (m-40) cc_final: 0.8755 (m-40) REVERT: G 199 GLU cc_start: 0.8032 (pt0) cc_final: 0.7711 (tp30) REVERT: G 203 ARG cc_start: 0.8915 (tpp-160) cc_final: 0.8260 (mtp-110) REVERT: G 214 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8237 (tm-30) REVERT: G 319 ASP cc_start: 0.8246 (m-30) cc_final: 0.7938 (m-30) REVERT: G 412 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7338 (ptt90) REVERT: G 483 MET cc_start: 0.9203 (tmm) cc_final: 0.8709 (tmm) REVERT: G 507 HIS cc_start: 0.8520 (t-90) cc_final: 0.8138 (t-90) REVERT: H 16 ASP cc_start: 0.8128 (t0) cc_final: 0.7907 (t0) REVERT: H 65 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8425 (mm) REVERT: H 70 MET cc_start: 0.9001 (ptt) cc_final: 0.8736 (ptt) REVERT: H 75 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6330 (pm20) REVERT: H 92 HIS cc_start: 0.8952 (p90) cc_final: 0.8683 (p-80) REVERT: H 134 LYS cc_start: 0.7987 (pttp) cc_final: 0.7775 (pttm) REVERT: H 179 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6978 (ppp) REVERT: H 214 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8336 (tm-30) REVERT: H 232 ASP cc_start: 0.8349 (t70) cc_final: 0.7960 (t70) REVERT: H 319 ASP cc_start: 0.8194 (m-30) cc_final: 0.7719 (m-30) REVERT: H 412 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7475 (ptt90) REVERT: H 507 HIS cc_start: 0.8545 (t-90) cc_final: 0.8189 (t-90) outliers start: 170 outliers final: 133 residues processed: 860 average time/residue: 0.4050 time to fit residues: 572.7916 Evaluate side-chains 905 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 750 time to evaluate : 3.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 312 ASN Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 184 ASP Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.3980 chunk 331 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 286 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 311 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104939 restraints weight = 54065.432| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.70 r_work: 0.3130 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32072 Z= 0.200 Angle : 0.678 9.596 43488 Z= 0.339 Chirality : 0.046 0.154 4968 Planarity : 0.004 0.036 5448 Dihedral : 12.148 85.977 5398 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.61 % Allowed : 27.96 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -1.56 (0.13), residues: 3968 helix: -0.20 (0.15), residues: 1256 sheet: -0.72 (0.26), residues: 424 loop : -1.62 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS D 92 PHE 0.008 0.001 PHE A 24 TYR 0.018 0.001 TYR B 233 ARG 0.005 0.000 ARG H 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9998.47 seconds wall clock time: 181 minutes 4.67 seconds (10864.67 seconds total)