Starting phenix.real_space_refine on Sun Apr 14 14:21:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9o_20701/04_2024/6u9o_20701_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9o_20701/04_2024/6u9o_20701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9o_20701/04_2024/6u9o_20701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9o_20701/04_2024/6u9o_20701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9o_20701/04_2024/6u9o_20701_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9o_20701/04_2024/6u9o_20701_updated.pdb" } resolution = 3.36 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= 0.068 sd= 2.635 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 96 5.49 5 S 176 5.16 5 C 19736 2.51 5 N 5440 2.21 5 O 6344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" 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 ARG 407": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" 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 ARG 407": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" 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 ARG 407": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" 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 ARG 407": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" 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 ARG 407": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" 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 ARG 407": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" 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 ARG 407": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" 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 ARG 407": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31792 Number of models: 1 Model: "" Number of chains: 24 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 16.84, per 1000 atoms: 0.53 Number of scatterers: 31792 At special positions: 0 Unit cell: (152.25, 152.25, 116.55, 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 96 15.00 O 6344 8.00 N 5440 7.00 C 19736 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.32 Conformation dependent library (CDL) restraints added in 5.8 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: 152 helices and 48 sheets defined 31.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' 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 76 through 84 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.514A pdb=" N PHE A 131 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 132 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.702A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.823A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.866A 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 356 removed outlier: 3.538A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' 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 76 through 84 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.515A pdb=" N PHE B 131 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 132 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.703A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.823A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.866A 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 356 removed outlier: 3.538A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' 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 76 through 84 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.515A pdb=" N PHE C 131 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 132 " --> pdb=" O ASP C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.702A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 3.822A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.866A 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 356 removed outlier: 3.538A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 497 through 501 Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' 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 76 through 84 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 137 removed outlier: 3.515A pdb=" N PHE D 131 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 132 " --> pdb=" O ASP D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.702A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.822A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.866A 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 356 removed outlier: 3.538A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'E' and resid 20 through 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' 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 76 through 84 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.515A pdb=" N PHE E 131 " --> pdb=" O ARG E 128 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU E 132 " --> pdb=" O ASP E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.702A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 3.822A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.865A 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 356 removed outlier: 3.538A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 453 through 455 No H-bonds generated for 'chain 'E' and resid 453 through 455' Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 497 through 501 Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' 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 76 through 84 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.514A pdb=" N PHE F 131 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU F 132 " --> pdb=" O ASP F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.702A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 3.822A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.865A 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 356 removed outlier: 3.538A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 453 through 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' Processing helix chain 'F' and resid 457 through 471 Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 497 through 501 Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' 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 76 through 84 Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.515A pdb=" N PHE G 131 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU G 132 " --> pdb=" O ASP G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.702A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 3.822A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.866A 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 356 removed outlier: 3.539A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 453 through 455 No H-bonds generated for 'chain 'G' and resid 453 through 455' Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 497 through 501 Processing helix chain 'H' and resid 20 through 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' 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 76 through 84 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.515A pdb=" N PHE H 131 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU H 132 " --> pdb=" O ASP H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.703A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 3.822A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.866A 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 356 removed outlier: 3.538A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 453 through 455 No H-bonds generated for 'chain 'H' and resid 453 through 455' Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 497 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 38 removed outlier: 4.606A pdb=" N LYS A 489 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 5.954A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 383 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.629A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (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 removed outlier: 3.841A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 35 through 38 removed outlier: 4.607A pdb=" N LYS B 489 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.955A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.629A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL B 272 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (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 removed outlier: 3.841A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 35 through 38 removed outlier: 4.606A pdb=" N LYS C 489 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 65 through 67 removed outlier: 5.954A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 383 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.628A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (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 removed outlier: 3.840A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 35 through 38 removed outlier: 4.607A pdb=" N LYS D 489 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 65 through 67 removed outlier: 5.955A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.629A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL D 272 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (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 removed outlier: 3.840A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 38 removed outlier: 4.605A pdb=" N LYS E 489 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 65 through 67 removed outlier: 5.954A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR E 383 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.629A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (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 removed outlier: 3.841A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 35 through 38 removed outlier: 4.606A pdb=" N LYS F 489 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 65 through 67 removed outlier: 5.954A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 383 " --> pdb=" O VAL F 361 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.630A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (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 removed outlier: 3.840A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 35 through 38 removed outlier: 4.606A pdb=" N LYS G 489 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 65 through 67 removed outlier: 5.954A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR G 383 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.629A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL G 272 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (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 removed outlier: 3.840A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 35 through 38 removed outlier: 4.605A pdb=" N LYS H 489 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.954A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR H 383 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.629A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (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 removed outlier: 3.840A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2064 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: 10.80 Time building geometry restraints manager: 14.07 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: 5337 1.30 - 1.43: 7871 1.43 - 1.56: 18600 1.56 - 1.69: 248 1.69 - 1.82: 296 Bond restraints: 32352 Sorted by residual: bond pdb=" C2' ATP H 603 " pdb=" C3' ATP H 603 " ideal model delta sigma weight residual 1.531 1.246 0.285 1.20e-02 6.94e+03 5.63e+02 bond pdb=" C2' ATP E 603 " pdb=" C3' ATP E 603 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.61e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.60e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.60e+02 bond pdb=" C2' ATP F 603 " pdb=" C3' ATP F 603 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.58e+02 ... (remaining 32347 not shown) Histogram of bond angle deviations from ideal: 97.56 - 106.54: 1025 106.54 - 115.52: 20253 115.52 - 124.50: 21996 124.50 - 133.48: 605 133.48 - 142.46: 57 Bond angle restraints: 43936 Sorted by residual: angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 121.24 18.63 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 121.25 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 121.26 18.61 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 121.28 18.59 1.00e+00 1.00e+00 3.46e+02 ... (remaining 43931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 18920 33.93 - 67.87: 784 67.87 - 101.80: 64 101.80 - 135.74: 16 135.74 - 169.67: 24 Dihedral angle restraints: 19808 sinusoidal: 8400 harmonic: 11408 Sorted by residual: dihedral pdb=" CA THR G 74 " pdb=" C THR G 74 " pdb=" N GLU G 75 " pdb=" CA GLU G 75 " ideal model delta harmonic sigma weight residual 180.00 142.19 37.81 0 5.00e+00 4.00e-02 5.72e+01 dihedral pdb=" CA THR A 74 " pdb=" C THR A 74 " pdb=" N GLU A 75 " pdb=" CA GLU A 75 " ideal model delta harmonic sigma weight residual 180.00 142.24 37.76 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA THR E 74 " pdb=" C THR E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta harmonic sigma weight residual 180.00 142.24 37.76 0 5.00e+00 4.00e-02 5.70e+01 ... (remaining 19805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3525 0.070 - 0.140: 1247 0.140 - 0.209: 188 0.209 - 0.279: 16 0.279 - 0.349: 24 Chirality restraints: 5000 Sorted by residual: chirality pdb=" C3D NAD D 605 " pdb=" C2D NAD D 605 " pdb=" C4D NAD D 605 " pdb=" O3D NAD D 605 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C3D NAD G 605 " pdb=" C2D NAD G 605 " pdb=" C4D NAD G 605 " pdb=" O3D NAD G 605 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C3D NAD B 605 " pdb=" C2D NAD B 605 " pdb=" C4D NAD B 605 " pdb=" O3D NAD B 605 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 4997 not shown) Planarity restraints: 5456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 109 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.39e+00 pdb=" C LYS B 109 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS B 109 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR B 110 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 109 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C LYS A 109 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS A 109 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 110 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 109 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C LYS G 109 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS G 109 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR G 110 " -0.018 2.00e-02 2.50e+03 ... (remaining 5453 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2679 2.72 - 3.27: 30756 3.27 - 3.81: 55431 3.81 - 4.36: 67184 4.36 - 4.90: 109526 Nonbonded interactions: 265576 Sorted by model distance: nonbonded pdb=" OE1 GLU B 500 " pdb=" OG1 THR C 31 " model vdw 2.177 2.440 nonbonded pdb=" OG1 THR A 31 " pdb=" OE1 GLU D 500 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR E 31 " pdb=" OE1 GLU H 500 " model vdw 2.207 2.440 nonbonded pdb=" OE1 GLU F 500 " pdb=" OG1 THR G 31 " model vdw 2.215 2.440 nonbonded pdb=" OE1 GLU E 500 " pdb=" OG1 THR F 31 " model vdw 2.224 2.440 ... (remaining 265571 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: 2.130 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: 8.570 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 83.790 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.310 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.018 0.287 32352 Z= 1.120 Angle : 1.663 20.547 43936 Z= 0.939 Chirality : 0.071 0.349 5000 Planarity : 0.007 0.043 5456 Dihedral : 18.440 169.672 12528 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 8.31 % Allowed : 8.80 % Favored : 82.89 % 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: -4.12 (0.11), residues: 3968 helix: -3.34 (0.09), residues: 1296 sheet: -2.04 (0.24), residues: 384 loop : -2.53 (0.11), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 92 PHE 0.027 0.004 PHE E 401 TYR 0.019 0.003 TYR F 411 ARG 0.022 0.002 ARG G 231 *********************** 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 1735 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1463 time to evaluate : 3.879 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: A 15 ASP cc_start: 0.8338 (t0) cc_final: 0.7959 (t0) REVERT: A 75 GLU cc_start: 0.8093 (mp0) cc_final: 0.7675 (mp0) REVERT: A 108 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.8926 (tppp) REVERT: A 111 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9020 (mm-30) REVERT: A 164 ASP cc_start: 0.7999 (t70) cc_final: 0.7171 (t70) REVERT: A 168 GLU cc_start: 0.8851 (mp0) cc_final: 0.8404 (pm20) REVERT: A 175 LEU cc_start: 0.9578 (mp) cc_final: 0.9357 (mp) REVERT: A 179 MET cc_start: 0.8551 (ptt) cc_final: 0.8258 (ptt) REVERT: A 209 LEU cc_start: 0.7900 (pp) cc_final: 0.7687 (pp) REVERT: A 216 ASP cc_start: 0.9084 (t70) cc_final: 0.8697 (t0) REVERT: A 222 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8047 (mm) REVERT: A 253 HIS cc_start: 0.7574 (m-70) cc_final: 0.6949 (m-70) REVERT: A 258 TYR cc_start: 0.8837 (t80) cc_final: 0.8598 (t80) REVERT: A 261 ASP cc_start: 0.8831 (p0) cc_final: 0.8234 (p0) REVERT: A 262 LEU cc_start: 0.9065 (mm) cc_final: 0.8823 (mp) REVERT: A 269 ASP cc_start: 0.8347 (m-30) cc_final: 0.8080 (m-30) REVERT: A 274 ASP cc_start: 0.8831 (t0) cc_final: 0.8589 (t0) REVERT: A 296 ASN cc_start: 0.9206 (p0) cc_final: 0.8998 (p0) REVERT: A 329 SER cc_start: 0.9377 (p) cc_final: 0.9117 (p) REVERT: A 330 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9115 (pp) REVERT: A 335 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 410 LYS cc_start: 0.7853 (pttt) cc_final: 0.7054 (mtpp) REVERT: A 411 TYR cc_start: 0.8797 (t80) cc_final: 0.8425 (t80) REVERT: B 15 ASP cc_start: 0.8293 (t0) cc_final: 0.8018 (t0) REVERT: B 75 GLU cc_start: 0.7960 (mp0) cc_final: 0.7568 (mp0) REVERT: B 108 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8938 (tppp) REVERT: B 128 ARG cc_start: 0.7887 (ptt-90) cc_final: 0.7240 (ptt-90) REVERT: B 164 ASP cc_start: 0.8122 (t70) cc_final: 0.6403 (t70) REVERT: B 168 GLU cc_start: 0.8773 (mp0) cc_final: 0.8309 (pm20) REVERT: B 175 LEU cc_start: 0.9455 (mp) cc_final: 0.9205 (mp) REVERT: B 179 MET cc_start: 0.8421 (ptt) cc_final: 0.8186 (ptt) REVERT: B 216 ASP cc_start: 0.9023 (t70) cc_final: 0.8593 (t0) REVERT: B 222 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8061 (mm) REVERT: B 253 HIS cc_start: 0.7484 (m-70) cc_final: 0.6937 (m-70) REVERT: B 258 TYR cc_start: 0.8667 (t80) cc_final: 0.8348 (t80) REVERT: B 269 ASP cc_start: 0.8274 (m-30) cc_final: 0.7978 (m-30) REVERT: B 312 ASN cc_start: 0.9203 (t0) cc_final: 0.8847 (t0) REVERT: B 329 SER cc_start: 0.9366 (p) cc_final: 0.9143 (p) REVERT: B 330 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9125 (pp) REVERT: B 410 LYS cc_start: 0.7791 (pttt) cc_final: 0.6929 (mtpp) REVERT: B 411 TYR cc_start: 0.8703 (t80) cc_final: 0.8423 (t80) REVERT: C 15 ASP cc_start: 0.8339 (t0) cc_final: 0.8000 (t0) REVERT: C 75 GLU cc_start: 0.8067 (mp0) cc_final: 0.7676 (mp0) REVERT: C 108 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.8962 (tppp) REVERT: C 111 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 164 ASP cc_start: 0.7983 (t70) cc_final: 0.7425 (t0) REVERT: C 168 GLU cc_start: 0.8763 (mp0) cc_final: 0.8266 (pm20) REVERT: C 179 MET cc_start: 0.8416 (ptt) cc_final: 0.8125 (ptt) REVERT: C 209 LEU cc_start: 0.7947 (pp) cc_final: 0.7730 (pp) REVERT: C 216 ASP cc_start: 0.9088 (t70) cc_final: 0.8609 (t0) REVERT: C 222 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8007 (mm) REVERT: C 253 HIS cc_start: 0.7679 (m-70) cc_final: 0.7079 (m-70) REVERT: C 258 TYR cc_start: 0.8823 (t80) cc_final: 0.8411 (t80) REVERT: C 261 ASP cc_start: 0.8752 (p0) cc_final: 0.8109 (p0) REVERT: C 262 LEU cc_start: 0.8995 (mm) cc_final: 0.8563 (tp) REVERT: C 269 ASP cc_start: 0.8289 (m-30) cc_final: 0.8040 (m-30) REVERT: C 274 ASP cc_start: 0.8845 (t0) cc_final: 0.8604 (t0) REVERT: C 330 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9153 (pp) REVERT: C 335 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6904 (mm-30) REVERT: C 410 LYS cc_start: 0.7858 (pttt) cc_final: 0.7068 (mtpp) REVERT: C 411 TYR cc_start: 0.8781 (t80) cc_final: 0.8429 (t80) REVERT: D 15 ASP cc_start: 0.8337 (t0) cc_final: 0.8063 (t0) REVERT: D 51 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8967 (pp) REVERT: D 75 GLU cc_start: 0.7976 (mp0) cc_final: 0.7571 (mp0) REVERT: D 102 ASN cc_start: 0.9153 (t0) cc_final: 0.8818 (t0) REVERT: D 108 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8946 (tppp) REVERT: D 128 ARG cc_start: 0.7885 (ptt-90) cc_final: 0.7268 (ptt-90) REVERT: D 164 ASP cc_start: 0.8095 (t70) cc_final: 0.7586 (t0) REVERT: D 168 GLU cc_start: 0.8799 (mp0) cc_final: 0.8354 (pm20) REVERT: D 175 LEU cc_start: 0.9519 (mp) cc_final: 0.9239 (mp) REVERT: D 179 MET cc_start: 0.8507 (ptt) cc_final: 0.8243 (ptt) REVERT: D 205 LYS cc_start: 0.9159 (mptm) cc_final: 0.8768 (mptt) REVERT: D 209 LEU cc_start: 0.7975 (pp) cc_final: 0.7768 (pp) REVERT: D 216 ASP cc_start: 0.9024 (t70) cc_final: 0.8637 (t0) REVERT: D 222 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8133 (mm) REVERT: D 253 HIS cc_start: 0.7607 (m-70) cc_final: 0.7042 (m-70) REVERT: D 269 ASP cc_start: 0.8286 (m-30) cc_final: 0.8059 (m-30) REVERT: D 274 ASP cc_start: 0.8797 (t0) cc_final: 0.8596 (t0) REVERT: D 312 ASN cc_start: 0.9194 (t0) cc_final: 0.8834 (t0) REVERT: D 329 SER cc_start: 0.9385 (p) cc_final: 0.9156 (p) REVERT: D 330 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9134 (pp) REVERT: D 335 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6900 (mm-30) REVERT: D 395 GLU cc_start: 0.8534 (mp0) cc_final: 0.8330 (mp0) REVERT: D 410 LYS cc_start: 0.7713 (pttt) cc_final: 0.6833 (mttp) REVERT: D 411 TYR cc_start: 0.8711 (t80) cc_final: 0.8375 (t80) REVERT: E 15 ASP cc_start: 0.8302 (t0) cc_final: 0.8029 (t0) REVERT: E 34 ASP cc_start: 0.8665 (p0) cc_final: 0.8420 (p0) REVERT: E 75 GLU cc_start: 0.8004 (mp0) cc_final: 0.7633 (mp0) REVERT: E 108 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.8941 (tppp) REVERT: E 111 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9012 (mm-30) REVERT: E 168 GLU cc_start: 0.8803 (mp0) cc_final: 0.8365 (pm20) REVERT: E 179 MET cc_start: 0.8367 (ptt) cc_final: 0.8090 (ptt) REVERT: E 209 LEU cc_start: 0.7917 (pp) cc_final: 0.7680 (pp) REVERT: E 216 ASP cc_start: 0.9079 (t70) cc_final: 0.8611 (t0) REVERT: E 222 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8030 (mm) REVERT: E 253 HIS cc_start: 0.7523 (m-70) cc_final: 0.6946 (m-70) REVERT: E 258 TYR cc_start: 0.8790 (t80) cc_final: 0.8474 (t80) REVERT: E 261 ASP cc_start: 0.8735 (p0) cc_final: 0.8034 (p0) REVERT: E 262 LEU cc_start: 0.9012 (mm) cc_final: 0.8606 (tp) REVERT: E 269 ASP cc_start: 0.8321 (m-30) cc_final: 0.8038 (m-30) REVERT: E 274 ASP cc_start: 0.8851 (t0) cc_final: 0.8636 (t0) REVERT: E 325 MET cc_start: 0.8739 (ttm) cc_final: 0.8428 (ttp) REVERT: E 329 SER cc_start: 0.9383 (p) cc_final: 0.9167 (p) REVERT: E 330 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9138 (pp) REVERT: E 335 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7185 (mm-30) REVERT: E 395 GLU cc_start: 0.8481 (mp0) cc_final: 0.8280 (mp0) REVERT: E 411 TYR cc_start: 0.8775 (t80) cc_final: 0.8452 (t80) REVERT: F 15 ASP cc_start: 0.8315 (t0) cc_final: 0.8056 (t0) REVERT: F 51 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8967 (pp) REVERT: F 75 GLU cc_start: 0.7914 (mp0) cc_final: 0.7535 (mp0) REVERT: F 105 ARG cc_start: 0.8133 (mtm110) cc_final: 0.7923 (ttp-110) REVERT: F 108 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8877 (tppp) REVERT: F 128 ARG cc_start: 0.7923 (ptt-90) cc_final: 0.7236 (ptt-90) REVERT: F 168 GLU cc_start: 0.8793 (mp0) cc_final: 0.8307 (pm20) REVERT: F 175 LEU cc_start: 0.9452 (mp) cc_final: 0.9200 (mp) REVERT: F 179 MET cc_start: 0.8445 (ptt) cc_final: 0.8201 (ptt) REVERT: F 216 ASP cc_start: 0.9045 (t70) cc_final: 0.8556 (t0) REVERT: F 222 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8050 (mm) REVERT: F 253 HIS cc_start: 0.7598 (m-70) cc_final: 0.6972 (m-70) REVERT: F 269 ASP cc_start: 0.8270 (m-30) cc_final: 0.8023 (m-30) REVERT: F 274 ASP cc_start: 0.8806 (t0) cc_final: 0.8600 (t0) REVERT: F 329 SER cc_start: 0.9389 (p) cc_final: 0.9141 (p) REVERT: F 330 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9145 (pp) REVERT: F 335 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6834 (mm-30) REVERT: F 395 GLU cc_start: 0.8472 (mp0) cc_final: 0.8249 (mp0) REVERT: F 411 TYR cc_start: 0.8719 (t80) cc_final: 0.8379 (t80) REVERT: F 505 SER cc_start: 0.9032 (t) cc_final: 0.8816 (p) REVERT: G 15 ASP cc_start: 0.8336 (t0) cc_final: 0.8087 (t0) REVERT: G 34 ASP cc_start: 0.8706 (p0) cc_final: 0.8482 (p0) REVERT: G 75 GLU cc_start: 0.8085 (mp0) cc_final: 0.7696 (mp0) REVERT: G 108 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.8931 (tppp) REVERT: G 111 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9042 (mm-30) REVERT: G 168 GLU cc_start: 0.8751 (mp0) cc_final: 0.8348 (pm20) REVERT: G 175 LEU cc_start: 0.9560 (mp) cc_final: 0.9336 (mp) REVERT: G 179 MET cc_start: 0.8533 (ptt) cc_final: 0.8266 (ptt) REVERT: G 209 LEU cc_start: 0.7868 (pp) cc_final: 0.7633 (pp) REVERT: G 216 ASP cc_start: 0.9072 (t70) cc_final: 0.8628 (t0) REVERT: G 222 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8029 (mm) REVERT: G 253 HIS cc_start: 0.7654 (m-70) cc_final: 0.7050 (m-70) REVERT: G 269 ASP cc_start: 0.8347 (m-30) cc_final: 0.8114 (m-30) REVERT: G 274 ASP cc_start: 0.8838 (t0) cc_final: 0.8593 (t0) REVERT: G 330 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9162 (pp) REVERT: G 335 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7132 (mm-30) REVERT: G 395 GLU cc_start: 0.8509 (mp0) cc_final: 0.8304 (mp0) REVERT: G 410 LYS cc_start: 0.7794 (pttt) cc_final: 0.6995 (mtpp) REVERT: G 411 TYR cc_start: 0.8746 (t80) cc_final: 0.8413 (t80) REVERT: O 1 MET cc_start: 0.5763 (pp-130) cc_final: 0.5550 (pmm) REVERT: H 15 ASP cc_start: 0.8320 (t0) cc_final: 0.8087 (t0) REVERT: H 51 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8859 (pp) REVERT: H 75 GLU cc_start: 0.7933 (mp0) cc_final: 0.7531 (mp0) REVERT: H 108 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8911 (tppp) REVERT: H 128 ARG cc_start: 0.7855 (ptt-90) cc_final: 0.7247 (ptt-90) REVERT: H 150 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8123 (tmm) REVERT: H 164 ASP cc_start: 0.8127 (t70) cc_final: 0.7642 (t0) REVERT: H 166 LEU cc_start: 0.8825 (mp) cc_final: 0.8457 (mt) REVERT: H 168 GLU cc_start: 0.8755 (mp0) cc_final: 0.8391 (pm20) REVERT: H 175 LEU cc_start: 0.9503 (mp) cc_final: 0.9263 (mp) REVERT: H 179 MET cc_start: 0.8495 (ptt) cc_final: 0.8264 (ptt) REVERT: H 216 ASP cc_start: 0.9079 (t70) cc_final: 0.8644 (t0) REVERT: H 222 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8088 (mm) REVERT: H 253 HIS cc_start: 0.7582 (m-70) cc_final: 0.6990 (m-70) REVERT: H 261 ASP cc_start: 0.8609 (p0) cc_final: 0.8367 (p0) REVERT: H 269 ASP cc_start: 0.8328 (m-30) cc_final: 0.8113 (m-30) REVERT: H 274 ASP cc_start: 0.8790 (t0) cc_final: 0.8590 (t0) REVERT: H 329 SER cc_start: 0.9362 (p) cc_final: 0.9085 (p) REVERT: H 330 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9127 (pp) REVERT: H 395 GLU cc_start: 0.8510 (mp0) cc_final: 0.8280 (mp0) REVERT: H 411 TYR cc_start: 0.8724 (t80) cc_final: 0.8418 (t80) REVERT: H 505 SER cc_start: 0.9032 (t) cc_final: 0.8718 (t) outliers start: 272 outliers final: 78 residues processed: 1516 average time/residue: 0.4174 time to fit residues: 1023.5600 Evaluate side-chains 1051 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 945 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 108 LYS Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 508 SER Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 178 ILE Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 467 SER Chi-restraints excluded: chain G residue 508 SER Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 222 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 508 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 101 optimal weight: 0.0370 chunk 200 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 355 optimal weight: 8.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 102 ASN A 230 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 102 ASN B 230 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 230 ASN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 230 ASN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN E 230 ASN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN F 230 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 230 ASN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN H 230 ASN ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32352 Z= 0.224 Angle : 0.699 6.934 43936 Z= 0.346 Chirality : 0.048 0.185 5000 Planarity : 0.004 0.034 5456 Dihedral : 17.336 161.479 5543 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 6.82 % Allowed : 19.04 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.63 (0.12), residues: 3968 helix: -1.56 (0.13), residues: 1216 sheet: -1.78 (0.20), residues: 584 loop : -1.82 (0.12), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 454 PHE 0.025 0.001 PHE B 401 TYR 0.014 0.001 TYR A 353 ARG 0.007 0.001 ARG D 224 *********************** 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 1314 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1091 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8491 (t0) cc_final: 0.8094 (t0) REVERT: A 34 ASP cc_start: 0.8582 (p0) cc_final: 0.8329 (p0) REVERT: A 43 ASP cc_start: 0.8713 (p0) cc_final: 0.8440 (p0) REVERT: A 105 ARG cc_start: 0.8456 (ttp-110) cc_final: 0.8204 (ttp-110) REVERT: A 168 GLU cc_start: 0.8786 (mp0) cc_final: 0.8370 (pm20) REVERT: A 175 LEU cc_start: 0.9549 (mp) cc_final: 0.9328 (mp) REVERT: A 179 MET cc_start: 0.8496 (ptt) cc_final: 0.8156 (ptt) REVERT: A 258 TYR cc_start: 0.8826 (t80) cc_final: 0.8260 (t80) REVERT: A 269 ASP cc_start: 0.8278 (m-30) cc_final: 0.8058 (m-30) REVERT: A 274 ASP cc_start: 0.8729 (t0) cc_final: 0.8458 (t0) REVERT: A 329 SER cc_start: 0.9425 (p) cc_final: 0.9201 (p) REVERT: A 330 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9076 (pp) REVERT: A 352 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 410 LYS cc_start: 0.7887 (pttt) cc_final: 0.7253 (mtpp) REVERT: A 512 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7692 (mtp85) REVERT: I 1 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.2926 (pp-130) REVERT: B 15 ASP cc_start: 0.8400 (t0) cc_final: 0.8036 (t70) REVERT: B 34 ASP cc_start: 0.8549 (p0) cc_final: 0.8291 (p0) REVERT: B 43 ASP cc_start: 0.8700 (p0) cc_final: 0.8400 (p0) REVERT: B 70 MET cc_start: 0.8388 (mpp) cc_final: 0.7713 (mpp) REVERT: B 105 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.8162 (ttp-110) REVERT: B 128 ARG cc_start: 0.7593 (ptt-90) cc_final: 0.7375 (ptt-90) REVERT: B 168 GLU cc_start: 0.8714 (mp0) cc_final: 0.8310 (pm20) REVERT: B 175 LEU cc_start: 0.9513 (mp) cc_final: 0.9222 (mp) REVERT: B 179 MET cc_start: 0.8360 (ptt) cc_final: 0.8080 (ptt) REVERT: B 329 SER cc_start: 0.9426 (p) cc_final: 0.9185 (p) REVERT: B 330 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.8998 (pp) REVERT: B 352 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 411 TYR cc_start: 0.8828 (t80) cc_final: 0.8152 (t80) REVERT: B 512 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7638 (mtp85) REVERT: C 15 ASP cc_start: 0.8517 (t0) cc_final: 0.8132 (t0) REVERT: C 34 ASP cc_start: 0.8586 (p0) cc_final: 0.8347 (p0) REVERT: C 43 ASP cc_start: 0.8777 (p0) cc_final: 0.8540 (p0) REVERT: C 70 MET cc_start: 0.8297 (mpp) cc_final: 0.7553 (mpp) REVERT: C 103 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: C 105 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8263 (ttp-110) REVERT: C 168 GLU cc_start: 0.8804 (mp0) cc_final: 0.8362 (pm20) REVERT: C 179 MET cc_start: 0.8375 (ptt) cc_final: 0.8015 (ptt) REVERT: C 205 LYS cc_start: 0.9034 (mptm) cc_final: 0.8664 (mptt) REVERT: C 258 TYR cc_start: 0.8824 (t80) cc_final: 0.8243 (t80) REVERT: C 269 ASP cc_start: 0.8265 (m-30) cc_final: 0.8043 (m-30) REVERT: C 274 ASP cc_start: 0.8685 (t0) cc_final: 0.8434 (t0) REVERT: C 329 SER cc_start: 0.9410 (p) cc_final: 0.9194 (p) REVERT: C 330 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.9029 (pp) REVERT: C 352 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8327 (tm-30) REVERT: C 410 LYS cc_start: 0.7901 (pttt) cc_final: 0.7435 (pttp) REVERT: C 411 TYR cc_start: 0.8906 (t80) cc_final: 0.8208 (t80) REVERT: C 512 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7794 (mtp85) REVERT: K 1 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.3004 (pp-130) REVERT: D 15 ASP cc_start: 0.8415 (t0) cc_final: 0.8051 (t0) REVERT: D 34 ASP cc_start: 0.8608 (p0) cc_final: 0.8369 (p0) REVERT: D 43 ASP cc_start: 0.8711 (p0) cc_final: 0.8391 (p0) REVERT: D 51 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8784 (pp) REVERT: D 70 MET cc_start: 0.8298 (mpp) cc_final: 0.7661 (mpp) REVERT: D 128 ARG cc_start: 0.7636 (ptt-90) cc_final: 0.7390 (ptt-90) REVERT: D 164 ASP cc_start: 0.7851 (t70) cc_final: 0.7535 (t0) REVERT: D 168 GLU cc_start: 0.8742 (mp0) cc_final: 0.8317 (pm20) REVERT: D 175 LEU cc_start: 0.9544 (mp) cc_final: 0.9275 (mp) REVERT: D 179 MET cc_start: 0.8508 (ptt) cc_final: 0.8211 (ptt) REVERT: D 205 LYS cc_start: 0.9143 (mptm) cc_final: 0.8703 (mptt) REVERT: D 259 ARG cc_start: 0.8306 (mtp85) cc_final: 0.8034 (ttm110) REVERT: D 274 ASP cc_start: 0.8605 (t0) cc_final: 0.8398 (t0) REVERT: D 279 ASN cc_start: 0.8466 (t0) cc_final: 0.8113 (t0) REVERT: D 329 SER cc_start: 0.9402 (p) cc_final: 0.9167 (p) REVERT: D 330 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9047 (pp) REVERT: D 352 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8317 (tm-30) REVERT: D 411 TYR cc_start: 0.8816 (t80) cc_final: 0.8211 (t80) REVERT: L 1 MET cc_start: 0.5351 (OUTLIER) cc_final: 0.4977 (pmm) REVERT: E 15 ASP cc_start: 0.8427 (t0) cc_final: 0.8066 (t70) REVERT: E 34 ASP cc_start: 0.8558 (p0) cc_final: 0.8321 (p0) REVERT: E 43 ASP cc_start: 0.8691 (p0) cc_final: 0.8435 (p0) REVERT: E 70 MET cc_start: 0.8308 (mpp) cc_final: 0.7586 (mpp) REVERT: E 168 GLU cc_start: 0.8697 (mp0) cc_final: 0.8294 (pm20) REVERT: E 179 MET cc_start: 0.8329 (ptt) cc_final: 0.8041 (ptt) REVERT: E 250 ILE cc_start: 0.8556 (pp) cc_final: 0.8344 (pp) REVERT: E 258 TYR cc_start: 0.8803 (t80) cc_final: 0.8289 (t80) REVERT: E 269 ASP cc_start: 0.8223 (m-30) cc_final: 0.7993 (m-30) REVERT: E 329 SER cc_start: 0.9374 (p) cc_final: 0.9138 (p) REVERT: E 330 ILE cc_start: 0.9482 (OUTLIER) cc_final: 0.9037 (pp) REVERT: E 352 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8300 (tm-30) REVERT: E 395 GLU cc_start: 0.8539 (mp0) cc_final: 0.8332 (mp0) REVERT: E 411 TYR cc_start: 0.8928 (t80) cc_final: 0.8292 (t80) REVERT: F 15 ASP cc_start: 0.8391 (t0) cc_final: 0.8041 (t70) REVERT: F 34 ASP cc_start: 0.8545 (p0) cc_final: 0.8306 (p0) REVERT: F 37 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8416 (mm) REVERT: F 43 ASP cc_start: 0.8754 (p0) cc_final: 0.8451 (p0) REVERT: F 51 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8832 (pp) REVERT: F 78 MET cc_start: 0.8924 (ttp) cc_final: 0.8575 (ttp) REVERT: F 128 ARG cc_start: 0.7643 (ptt-90) cc_final: 0.7333 (ptt-90) REVERT: F 168 GLU cc_start: 0.8731 (mp0) cc_final: 0.8340 (pm20) REVERT: F 175 LEU cc_start: 0.9473 (mp) cc_final: 0.9179 (mp) REVERT: F 179 MET cc_start: 0.8407 (ptt) cc_final: 0.8131 (ptt) REVERT: F 272 VAL cc_start: 0.8616 (t) cc_final: 0.8075 (p) REVERT: F 274 ASP cc_start: 0.8687 (t0) cc_final: 0.8447 (t0) REVERT: F 329 SER cc_start: 0.9406 (p) cc_final: 0.9175 (p) REVERT: F 330 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9045 (pp) REVERT: F 352 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8362 (tm-30) REVERT: F 395 GLU cc_start: 0.8513 (mp0) cc_final: 0.8267 (mp0) REVERT: F 411 TYR cc_start: 0.8837 (t80) cc_final: 0.8344 (t80) REVERT: F 505 SER cc_start: 0.8991 (t) cc_final: 0.8657 (t) REVERT: N 1 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.2708 (pp-130) REVERT: G 15 ASP cc_start: 0.8427 (t0) cc_final: 0.8082 (t70) REVERT: G 34 ASP cc_start: 0.8634 (p0) cc_final: 0.8400 (p0) REVERT: G 37 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8555 (mm) REVERT: G 43 ASP cc_start: 0.8704 (p0) cc_final: 0.8454 (p0) REVERT: G 78 MET cc_start: 0.8867 (ttp) cc_final: 0.8623 (ttp) REVERT: G 103 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: G 168 GLU cc_start: 0.8743 (mp0) cc_final: 0.8399 (pm20) REVERT: G 175 LEU cc_start: 0.9546 (mp) cc_final: 0.9291 (mp) REVERT: G 179 MET cc_start: 0.8489 (ptt) cc_final: 0.8201 (ptt) REVERT: G 259 ARG cc_start: 0.8408 (mtp85) cc_final: 0.8154 (ttm110) REVERT: G 265 GLN cc_start: 0.9087 (mm110) cc_final: 0.8775 (mp10) REVERT: G 274 ASP cc_start: 0.8664 (t0) cc_final: 0.8404 (t0) REVERT: G 330 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9085 (pp) REVERT: G 352 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8356 (tm-30) REVERT: G 395 GLU cc_start: 0.8573 (mp0) cc_final: 0.8321 (mp0) REVERT: G 411 TYR cc_start: 0.8890 (t80) cc_final: 0.8419 (t80) REVERT: O 1 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5384 (pmm) REVERT: H 15 ASP cc_start: 0.8459 (t0) cc_final: 0.8135 (t70) REVERT: H 34 ASP cc_start: 0.8513 (p0) cc_final: 0.8282 (p0) REVERT: H 37 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8389 (mm) REVERT: H 43 ASP cc_start: 0.8699 (p0) cc_final: 0.8417 (p0) REVERT: H 51 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8752 (pp) REVERT: H 75 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7638 (mp0) REVERT: H 78 MET cc_start: 0.8899 (ttp) cc_final: 0.8555 (ttp) REVERT: H 105 ARG cc_start: 0.8502 (ttp-110) cc_final: 0.8271 (ttp-110) REVERT: H 128 ARG cc_start: 0.7697 (ptt-90) cc_final: 0.7435 (ptt-90) REVERT: H 168 GLU cc_start: 0.8728 (mp0) cc_final: 0.8360 (pm20) REVERT: H 175 LEU cc_start: 0.9558 (mp) cc_final: 0.9279 (mp) REVERT: H 179 MET cc_start: 0.8471 (ptt) cc_final: 0.8201 (ptt) REVERT: H 330 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9059 (pp) REVERT: H 352 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8432 (tm-30) REVERT: H 395 GLU cc_start: 0.8541 (mp0) cc_final: 0.8285 (mp0) REVERT: H 411 TYR cc_start: 0.8858 (t80) cc_final: 0.8512 (t80) REVERT: H 505 SER cc_start: 0.8937 (t) cc_final: 0.8668 (t) REVERT: P 1 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.2703 (pp-130) outliers start: 223 outliers final: 103 residues processed: 1197 average time/residue: 0.4182 time to fit residues: 812.3758 Evaluate side-chains 1044 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 919 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 296 optimal weight: 0.5980 chunk 242 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 385 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 353 optimal weight: 0.0470 chunk 121 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 309 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN E 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN G 309 GLN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32352 Z= 0.292 Angle : 0.702 7.791 43936 Z= 0.342 Chirality : 0.048 0.187 5000 Planarity : 0.004 0.042 5456 Dihedral : 16.536 167.356 5376 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 7.33 % Allowed : 21.52 % Favored : 71.15 % 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: -2.11 (0.13), residues: 3968 helix: -1.14 (0.13), residues: 1296 sheet: -1.29 (0.24), residues: 456 loop : -1.58 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 454 PHE 0.034 0.002 PHE B 401 TYR 0.016 0.002 TYR A 353 ARG 0.008 0.001 ARG H 480 *********************** 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 1180 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 940 time to evaluate : 4.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8536 (t0) cc_final: 0.8200 (t0) REVERT: A 34 ASP cc_start: 0.8542 (p0) cc_final: 0.8330 (p0) REVERT: A 43 ASP cc_start: 0.8830 (p0) cc_final: 0.8607 (p0) REVERT: A 78 MET cc_start: 0.8822 (ttp) cc_final: 0.8483 (tmm) REVERT: A 128 ARG cc_start: 0.8816 (mtm180) cc_final: 0.8531 (mtm-85) REVERT: A 150 MET cc_start: 0.8273 (tmm) cc_final: 0.7876 (tmm) REVERT: A 168 GLU cc_start: 0.8821 (mp0) cc_final: 0.8378 (pm20) REVERT: A 179 MET cc_start: 0.8640 (ptt) cc_final: 0.8397 (ptt) REVERT: A 231 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8524 (ttp80) REVERT: A 269 ASP cc_start: 0.8357 (m-30) cc_final: 0.8140 (m-30) REVERT: A 272 VAL cc_start: 0.8790 (t) cc_final: 0.8317 (p) REVERT: A 330 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9133 (pp) REVERT: A 337 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8184 (tp) REVERT: A 352 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8385 (tm-30) REVERT: I 1 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.2850 (pp-130) REVERT: B 15 ASP cc_start: 0.8471 (t0) cc_final: 0.8185 (t70) REVERT: B 43 ASP cc_start: 0.8835 (p0) cc_final: 0.8554 (p0) REVERT: B 70 MET cc_start: 0.8547 (mpp) cc_final: 0.8091 (mpp) REVERT: B 128 ARG cc_start: 0.7651 (ptt-90) cc_final: 0.7404 (ptt-90) REVERT: B 168 GLU cc_start: 0.8785 (mp0) cc_final: 0.8384 (pm20) REVERT: B 175 LEU cc_start: 0.9557 (mp) cc_final: 0.9310 (mp) REVERT: B 202 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8784 (mt0) REVERT: B 272 VAL cc_start: 0.8572 (t) cc_final: 0.8121 (p) REVERT: B 330 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9121 (pp) REVERT: B 337 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7996 (tp) REVERT: B 512 ARG cc_start: 0.8381 (ttp-170) cc_final: 0.7491 (mtp85) REVERT: C 15 ASP cc_start: 0.8466 (t0) cc_final: 0.8117 (t0) REVERT: C 70 MET cc_start: 0.8311 (mpp) cc_final: 0.7907 (mpp) REVERT: C 78 MET cc_start: 0.8846 (ttp) cc_final: 0.8480 (tmm) REVERT: C 128 ARG cc_start: 0.8835 (mtm180) cc_final: 0.8496 (mtm-85) REVERT: C 168 GLU cc_start: 0.8784 (mp0) cc_final: 0.8272 (pm20) REVERT: C 258 TYR cc_start: 0.8742 (t80) cc_final: 0.8527 (t80) REVERT: C 269 ASP cc_start: 0.8351 (m-30) cc_final: 0.8133 (m-30) REVERT: C 272 VAL cc_start: 0.8768 (t) cc_final: 0.8326 (p) REVERT: C 330 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9147 (pp) REVERT: C 337 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7957 (tp) REVERT: C 352 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8420 (tm-30) REVERT: C 512 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.7662 (mtp85) REVERT: K 1 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.3060 (pp-130) REVERT: D 15 ASP cc_start: 0.8494 (t0) cc_final: 0.8171 (t70) REVERT: D 37 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8134 (mm) REVERT: D 38 LEU cc_start: 0.9346 (mt) cc_final: 0.9145 (mt) REVERT: D 51 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8845 (pp) REVERT: D 128 ARG cc_start: 0.7780 (ptt-90) cc_final: 0.7492 (ptt-90) REVERT: D 150 MET cc_start: 0.8302 (tmm) cc_final: 0.7815 (tmm) REVERT: D 168 GLU cc_start: 0.8764 (mp0) cc_final: 0.8312 (pm20) REVERT: D 175 LEU cc_start: 0.9624 (mp) cc_final: 0.9377 (mp) REVERT: D 330 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9129 (pp) REVERT: D 337 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8022 (tp) REVERT: D 512 ARG cc_start: 0.8337 (mtp180) cc_final: 0.7870 (mtp85) REVERT: L 1 MET cc_start: 0.5517 (OUTLIER) cc_final: 0.5036 (pmm) REVERT: E 15 ASP cc_start: 0.8498 (t0) cc_final: 0.8229 (t70) REVERT: E 78 MET cc_start: 0.9027 (ttp) cc_final: 0.8803 (ttp) REVERT: E 128 ARG cc_start: 0.8753 (mtm180) cc_final: 0.8530 (mtm-85) REVERT: E 168 GLU cc_start: 0.8790 (mp0) cc_final: 0.8364 (pm20) REVERT: E 258 TYR cc_start: 0.8698 (t80) cc_final: 0.8440 (t80) REVERT: E 272 VAL cc_start: 0.8710 (t) cc_final: 0.8259 (p) REVERT: E 329 SER cc_start: 0.9392 (p) cc_final: 0.9159 (p) REVERT: E 330 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9110 (pp) REVERT: E 337 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8136 (tp) REVERT: E 352 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8441 (tm-30) REVERT: E 395 GLU cc_start: 0.8494 (mp0) cc_final: 0.8263 (mp0) REVERT: F 15 ASP cc_start: 0.8462 (t0) cc_final: 0.8148 (t70) REVERT: F 37 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8224 (mm) REVERT: F 38 LEU cc_start: 0.9367 (mt) cc_final: 0.9139 (mt) REVERT: F 51 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9006 (pp) REVERT: F 78 MET cc_start: 0.8700 (ttp) cc_final: 0.8306 (tmm) REVERT: F 128 ARG cc_start: 0.7797 (ptt-90) cc_final: 0.7431 (ptt-90) REVERT: F 168 GLU cc_start: 0.8742 (mp0) cc_final: 0.8313 (pm20) REVERT: F 286 MET cc_start: 0.8922 (tpp) cc_final: 0.8719 (tpp) REVERT: F 330 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9136 (pp) REVERT: F 337 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7923 (tp) REVERT: F 395 GLU cc_start: 0.8531 (mp0) cc_final: 0.8199 (mp0) REVERT: F 505 SER cc_start: 0.8991 (t) cc_final: 0.8710 (t) REVERT: N 1 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.2787 (pp-130) REVERT: G 15 ASP cc_start: 0.8511 (t0) cc_final: 0.8254 (t70) REVERT: G 34 ASP cc_start: 0.8508 (p0) cc_final: 0.8303 (p0) REVERT: G 37 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8381 (mm) REVERT: G 78 MET cc_start: 0.8649 (ttp) cc_final: 0.8371 (tmm) REVERT: G 128 ARG cc_start: 0.8821 (mtm180) cc_final: 0.8507 (mtm-85) REVERT: G 150 MET cc_start: 0.8331 (tmm) cc_final: 0.7824 (tmm) REVERT: G 168 GLU cc_start: 0.8826 (mp0) cc_final: 0.8481 (pm20) REVERT: G 179 MET cc_start: 0.8633 (ptt) cc_final: 0.8387 (ptt) REVERT: G 259 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8202 (ttm110) REVERT: G 265 GLN cc_start: 0.9154 (mm110) cc_final: 0.8929 (mp10) REVERT: G 272 VAL cc_start: 0.8758 (t) cc_final: 0.8292 (p) REVERT: G 330 ILE cc_start: 0.9481 (OUTLIER) cc_final: 0.9162 (pp) REVERT: G 337 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8091 (tp) REVERT: G 352 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8474 (tm-30) REVERT: G 395 GLU cc_start: 0.8576 (mp0) cc_final: 0.8231 (mp0) REVERT: O 1 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5391 (pmm) REVERT: H 15 ASP cc_start: 0.8467 (t0) cc_final: 0.8167 (t70) REVERT: H 37 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8248 (mm) REVERT: H 43 ASP cc_start: 0.8777 (p0) cc_final: 0.8570 (p0) REVERT: H 78 MET cc_start: 0.8635 (ttp) cc_final: 0.8351 (tmm) REVERT: H 128 ARG cc_start: 0.7855 (ptt-90) cc_final: 0.7539 (ptt-90) REVERT: H 150 MET cc_start: 0.8351 (tmm) cc_final: 0.7974 (tmm) REVERT: H 168 GLU cc_start: 0.8783 (mp0) cc_final: 0.8390 (pm20) REVERT: H 175 LEU cc_start: 0.9623 (mp) cc_final: 0.9390 (mp) REVERT: H 330 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9136 (pp) REVERT: H 337 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8156 (tp) REVERT: H 352 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8505 (tm-30) REVERT: H 395 GLU cc_start: 0.8558 (mp0) cc_final: 0.8215 (mp0) REVERT: H 505 SER cc_start: 0.8956 (t) cc_final: 0.8709 (t) REVERT: P 1 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.3010 (pp-130) outliers start: 240 outliers final: 153 residues processed: 1073 average time/residue: 0.4267 time to fit residues: 752.0954 Evaluate side-chains 1047 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 865 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 466 HIS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 0.9980 chunk 268 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 239 optimal weight: 0.8980 chunk 357 optimal weight: 7.9990 chunk 378 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** B 283 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN G 202 GLN G 283 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32352 Z= 0.230 Angle : 0.663 7.828 43936 Z= 0.318 Chirality : 0.047 0.165 5000 Planarity : 0.004 0.044 5456 Dihedral : 16.105 167.605 5358 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 7.06 % Allowed : 22.92 % Favored : 70.02 % 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: -1.77 (0.13), residues: 3968 helix: -0.74 (0.14), residues: 1272 sheet: -1.43 (0.23), residues: 488 loop : -1.35 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 466 PHE 0.029 0.001 PHE B 401 TYR 0.015 0.001 TYR G 353 ARG 0.006 0.001 ARG A 105 *********************** 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 1190 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 959 time to evaluate : 3.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8587 (t0) cc_final: 0.8327 (t0) REVERT: A 16 ASP cc_start: 0.8383 (t0) cc_final: 0.8157 (t0) REVERT: A 128 ARG cc_start: 0.8882 (mtm180) cc_final: 0.8597 (mtm-85) REVERT: A 168 GLU cc_start: 0.8886 (mp0) cc_final: 0.8430 (pm20) REVERT: A 179 MET cc_start: 0.8577 (ptt) cc_final: 0.8265 (ptt) REVERT: A 205 LYS cc_start: 0.8965 (mmtm) cc_final: 0.8764 (mptt) REVERT: A 258 TYR cc_start: 0.8816 (t80) cc_final: 0.8432 (t80) REVERT: A 330 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9125 (pp) REVERT: A 337 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8033 (tp) REVERT: A 352 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 414 MET cc_start: 0.9027 (mmm) cc_final: 0.8782 (mmm) REVERT: A 512 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7498 (mtp85) REVERT: I 1 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.2954 (pp-130) REVERT: B 15 ASP cc_start: 0.8504 (t0) cc_final: 0.8235 (t0) REVERT: B 38 LEU cc_start: 0.9200 (mt) cc_final: 0.8967 (mt) REVERT: B 59 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8663 (pt) REVERT: B 78 MET cc_start: 0.8656 (ttp) cc_final: 0.8391 (ttp) REVERT: B 98 GLU cc_start: 0.9083 (mp0) cc_final: 0.8796 (mp0) REVERT: B 128 ARG cc_start: 0.7767 (ptt-90) cc_final: 0.7431 (ptt-90) REVERT: B 168 GLU cc_start: 0.8815 (mp0) cc_final: 0.8398 (pm20) REVERT: B 175 LEU cc_start: 0.9535 (mp) cc_final: 0.9274 (mp) REVERT: B 286 MET cc_start: 0.8894 (tpp) cc_final: 0.8693 (tpp) REVERT: B 330 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9152 (pp) REVERT: B 337 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7889 (tp) REVERT: B 512 ARG cc_start: 0.8275 (ttp-170) cc_final: 0.8046 (ttt180) REVERT: C 15 ASP cc_start: 0.8517 (t0) cc_final: 0.8293 (t70) REVERT: C 128 ARG cc_start: 0.8852 (mtm180) cc_final: 0.8517 (mtm-85) REVERT: C 168 GLU cc_start: 0.8819 (mp0) cc_final: 0.8309 (pm20) REVERT: C 179 MET cc_start: 0.8629 (ptt) cc_final: 0.8374 (ptt) REVERT: C 272 VAL cc_start: 0.8705 (t) cc_final: 0.8286 (p) REVERT: C 330 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9152 (pp) REVERT: C 337 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7989 (tp) REVERT: C 352 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8407 (tm-30) REVERT: C 512 ARG cc_start: 0.8244 (ttp-170) cc_final: 0.7556 (mtp85) REVERT: K 1 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.3235 (pp-130) REVERT: D 15 ASP cc_start: 0.8497 (t0) cc_final: 0.8210 (t0) REVERT: D 37 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7903 (mm) REVERT: D 51 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8743 (pp) REVERT: D 128 ARG cc_start: 0.7831 (ptt-90) cc_final: 0.7484 (ptt-90) REVERT: D 168 GLU cc_start: 0.8806 (mp0) cc_final: 0.8351 (pm20) REVERT: D 179 MET cc_start: 0.8715 (ptt) cc_final: 0.8502 (ptt) REVERT: D 205 LYS cc_start: 0.9054 (mmtm) cc_final: 0.8839 (mptt) REVERT: D 330 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9167 (pp) REVERT: D 337 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7954 (tp) REVERT: D 352 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8275 (tm-30) REVERT: D 414 MET cc_start: 0.9026 (mmm) cc_final: 0.8778 (mmm) REVERT: D 512 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7857 (mtp85) REVERT: L 1 MET cc_start: 0.5635 (OUTLIER) cc_final: 0.2726 (pp-130) REVERT: E 15 ASP cc_start: 0.8472 (t0) cc_final: 0.8226 (t0) REVERT: E 16 ASP cc_start: 0.8386 (t0) cc_final: 0.8147 (t0) REVERT: E 78 MET cc_start: 0.8833 (ttp) cc_final: 0.8216 (tmm) REVERT: E 168 GLU cc_start: 0.8859 (mp0) cc_final: 0.8439 (pm20) REVERT: E 179 MET cc_start: 0.8604 (ptt) cc_final: 0.8367 (ptt) REVERT: E 272 VAL cc_start: 0.8660 (t) cc_final: 0.8246 (p) REVERT: E 329 SER cc_start: 0.9395 (p) cc_final: 0.9156 (p) REVERT: E 330 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9122 (pp) REVERT: E 337 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8033 (tp) REVERT: E 352 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8478 (tm-30) REVERT: E 395 GLU cc_start: 0.8564 (mp0) cc_final: 0.8343 (mp0) REVERT: F 15 ASP cc_start: 0.8450 (t0) cc_final: 0.8177 (t0) REVERT: F 37 ILE cc_start: 0.8288 (mm) cc_final: 0.8085 (mm) REVERT: F 43 ASP cc_start: 0.8872 (p0) cc_final: 0.8662 (p0) REVERT: F 51 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8928 (pp) REVERT: F 98 GLU cc_start: 0.9074 (mp0) cc_final: 0.8767 (mp0) REVERT: F 128 ARG cc_start: 0.7800 (ptt-90) cc_final: 0.7375 (ptt-90) REVERT: F 168 GLU cc_start: 0.8778 (mp0) cc_final: 0.8357 (pm20) REVERT: F 175 LEU cc_start: 0.9518 (mp) cc_final: 0.9311 (mp) REVERT: F 224 ARG cc_start: 0.8899 (ptm160) cc_final: 0.8504 (ptm160) REVERT: F 330 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9127 (pp) REVERT: F 337 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7845 (tp) REVERT: F 352 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8308 (tm-30) REVERT: F 395 GLU cc_start: 0.8500 (mp0) cc_final: 0.8167 (mp0) REVERT: F 505 SER cc_start: 0.8984 (t) cc_final: 0.8713 (t) REVERT: N 1 MET cc_start: 0.5815 (OUTLIER) cc_final: 0.2919 (pp-130) REVERT: G 15 ASP cc_start: 0.8460 (t0) cc_final: 0.8219 (t70) REVERT: G 37 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8252 (mm) REVERT: G 59 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8824 (pt) REVERT: G 128 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8496 (mtm-85) REVERT: G 168 GLU cc_start: 0.8867 (mp0) cc_final: 0.8480 (pm20) REVERT: G 179 MET cc_start: 0.8503 (ptt) cc_final: 0.8205 (ptt) REVERT: G 265 GLN cc_start: 0.9166 (mm110) cc_final: 0.8890 (mp10) REVERT: G 330 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9131 (pp) REVERT: G 337 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8090 (tp) REVERT: G 352 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8441 (tm-30) REVERT: G 395 GLU cc_start: 0.8519 (mp0) cc_final: 0.8184 (mp0) REVERT: O 1 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.5179 (pmm) REVERT: H 15 ASP cc_start: 0.8495 (t0) cc_final: 0.8272 (t70) REVERT: H 37 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8118 (mm) REVERT: H 98 GLU cc_start: 0.9112 (mp0) cc_final: 0.8817 (mp0) REVERT: H 128 ARG cc_start: 0.7890 (ptt-90) cc_final: 0.7552 (ptt-90) REVERT: H 168 GLU cc_start: 0.8822 (mp0) cc_final: 0.8412 (pm20) REVERT: H 175 LEU cc_start: 0.9578 (mp) cc_final: 0.9377 (mp) REVERT: H 330 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9106 (pp) REVERT: H 337 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7808 (tp) REVERT: H 352 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8485 (tm-30) REVERT: H 395 GLU cc_start: 0.8503 (mp0) cc_final: 0.8200 (mp0) REVERT: H 505 SER cc_start: 0.8959 (t) cc_final: 0.8713 (t) REVERT: P 1 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.3129 (pp-130) outliers start: 231 outliers final: 143 residues processed: 1089 average time/residue: 0.4203 time to fit residues: 749.7844 Evaluate side-chains 1054 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 882 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.9990 chunk 215 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 323 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 340 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN D 94 ASN D 283 GLN D 309 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN F 94 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 GLN ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32352 Z= 0.169 Angle : 0.653 8.260 43936 Z= 0.310 Chirality : 0.046 0.170 5000 Planarity : 0.004 0.034 5456 Dihedral : 15.667 168.101 5358 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 6.08 % Allowed : 25.76 % Favored : 68.15 % 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: -1.58 (0.13), residues: 3968 helix: -0.59 (0.14), residues: 1296 sheet: -1.48 (0.23), residues: 488 loop : -1.18 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 466 PHE 0.025 0.001 PHE B 401 TYR 0.013 0.001 TYR H 353 ARG 0.007 0.001 ARG E 512 *********************** 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 1188 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 989 time to evaluate : 3.615 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: A 15 ASP cc_start: 0.8563 (t0) cc_final: 0.8339 (t0) REVERT: A 16 ASP cc_start: 0.8352 (t0) cc_final: 0.8140 (t0) REVERT: A 51 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8711 (pp) REVERT: A 75 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8120 (mm-30) REVERT: A 124 LYS cc_start: 0.9110 (mmmt) cc_final: 0.8867 (tppt) REVERT: A 150 MET cc_start: 0.8254 (tmm) cc_final: 0.7678 (tmm) REVERT: A 168 GLU cc_start: 0.8897 (mp0) cc_final: 0.8451 (pm20) REVERT: A 179 MET cc_start: 0.8620 (ptt) cc_final: 0.8360 (ptm) REVERT: A 216 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8706 (t0) REVERT: A 226 ASP cc_start: 0.9052 (m-30) cc_final: 0.8849 (m-30) REVERT: A 253 HIS cc_start: 0.7490 (m-70) cc_final: 0.7130 (m-70) REVERT: A 258 TYR cc_start: 0.8891 (t80) cc_final: 0.8463 (t80) REVERT: A 330 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9110 (pp) REVERT: A 337 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8061 (tp) REVERT: A 352 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8355 (tm-30) REVERT: I 1 MET cc_start: 0.5834 (OUTLIER) cc_final: 0.2926 (pp-130) REVERT: B 15 ASP cc_start: 0.8465 (t0) cc_final: 0.8250 (t0) REVERT: B 51 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8758 (pp) REVERT: B 59 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8523 (pt) REVERT: B 128 ARG cc_start: 0.7796 (ptt-90) cc_final: 0.7449 (ptt-90) REVERT: B 168 GLU cc_start: 0.8871 (mp0) cc_final: 0.8476 (pm20) REVERT: B 175 LEU cc_start: 0.9471 (mp) cc_final: 0.9263 (mp) REVERT: B 224 ARG cc_start: 0.8698 (ttt90) cc_final: 0.8305 (ttt90) REVERT: B 226 ASP cc_start: 0.9022 (m-30) cc_final: 0.8800 (m-30) REVERT: B 250 ILE cc_start: 0.8195 (pp) cc_final: 0.7912 (pp) REVERT: B 254 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 259 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8138 (ttm110) REVERT: B 330 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9145 (pp) REVERT: B 337 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7869 (tp) REVERT: B 512 ARG cc_start: 0.8223 (ttp-170) cc_final: 0.7488 (mtp85) REVERT: C 15 ASP cc_start: 0.8416 (t0) cc_final: 0.8155 (t70) REVERT: C 98 GLU cc_start: 0.9073 (mp0) cc_final: 0.8792 (mp0) REVERT: C 128 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8510 (mtm-85) REVERT: C 150 MET cc_start: 0.8276 (tmm) cc_final: 0.7689 (tmm) REVERT: C 168 GLU cc_start: 0.8848 (mp0) cc_final: 0.8391 (pm20) REVERT: C 205 LYS cc_start: 0.9235 (mptt) cc_final: 0.8818 (mmtm) REVERT: C 253 HIS cc_start: 0.7510 (m-70) cc_final: 0.7167 (m-70) REVERT: C 272 VAL cc_start: 0.8653 (t) cc_final: 0.8229 (p) REVERT: C 330 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9142 (pp) REVERT: C 337 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7963 (tp) REVERT: C 352 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8329 (tm-30) REVERT: C 459 TYR cc_start: 0.8888 (t80) cc_final: 0.8641 (t80) REVERT: C 512 ARG cc_start: 0.8181 (ttp-170) cc_final: 0.7590 (mtp85) REVERT: K 1 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.3114 (pp-130) REVERT: D 15 ASP cc_start: 0.8485 (t0) cc_final: 0.8255 (t70) REVERT: D 37 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7459 (mm) REVERT: D 51 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8550 (pp) REVERT: D 98 GLU cc_start: 0.9024 (mp0) cc_final: 0.8710 (mp0) REVERT: D 128 ARG cc_start: 0.7740 (ptt-90) cc_final: 0.7399 (ptt-90) REVERT: D 150 MET cc_start: 0.8181 (tmm) cc_final: 0.7614 (tmm) REVERT: D 168 GLU cc_start: 0.8857 (mp0) cc_final: 0.8399 (pm20) REVERT: D 206 LYS cc_start: 0.8140 (mmpt) cc_final: 0.7833 (mmmt) REVERT: D 254 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8285 (tm-30) REVERT: D 330 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9160 (pp) REVERT: D 337 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7914 (tp) REVERT: D 512 ARG cc_start: 0.8401 (mtp180) cc_final: 0.8012 (mtp85) REVERT: L 1 MET cc_start: 0.5634 (OUTLIER) cc_final: 0.2756 (pp-130) REVERT: E 75 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8122 (mm-30) REVERT: E 78 MET cc_start: 0.8543 (ttp) cc_final: 0.8284 (tmm) REVERT: E 94 ASN cc_start: 0.8587 (t0) cc_final: 0.8310 (t0) REVERT: E 128 ARG cc_start: 0.8771 (mtm180) cc_final: 0.8424 (mtm-85) REVERT: E 168 GLU cc_start: 0.8882 (mp0) cc_final: 0.8460 (pm20) REVERT: E 272 VAL cc_start: 0.8587 (t) cc_final: 0.8138 (p) REVERT: E 325 MET cc_start: 0.8279 (ttm) cc_final: 0.8053 (ttt) REVERT: E 330 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9200 (pp) REVERT: E 337 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8018 (tp) REVERT: E 352 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8421 (tm-30) REVERT: E 395 GLU cc_start: 0.8530 (mp0) cc_final: 0.8300 (mp0) REVERT: F 37 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7803 (mm) REVERT: F 51 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8814 (pp) REVERT: F 59 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8780 (pt) REVERT: F 75 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7962 (mm-30) REVERT: F 105 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8198 (ttp-110) REVERT: F 128 ARG cc_start: 0.7771 (ptt-90) cc_final: 0.7328 (ptt-90) REVERT: F 150 MET cc_start: 0.8242 (tmm) cc_final: 0.7658 (tmm) REVERT: F 168 GLU cc_start: 0.8844 (mp0) cc_final: 0.8386 (pm20) REVERT: F 175 LEU cc_start: 0.9455 (mp) cc_final: 0.9178 (mp) REVERT: F 179 MET cc_start: 0.8371 (ptt) cc_final: 0.8124 (ptp) REVERT: F 224 ARG cc_start: 0.8847 (ptm160) cc_final: 0.8473 (ptm160) REVERT: F 226 ASP cc_start: 0.9023 (m-30) cc_final: 0.8793 (m-30) REVERT: F 254 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 330 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9101 (pp) REVERT: F 337 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7701 (tp) REVERT: F 352 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8251 (tm-30) REVERT: F 395 GLU cc_start: 0.8447 (mp0) cc_final: 0.8164 (mp0) REVERT: F 505 SER cc_start: 0.8958 (t) cc_final: 0.8682 (t) REVERT: N 1 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.3034 (pp-130) REVERT: G 75 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8030 (mm-30) REVERT: G 98 GLU cc_start: 0.9068 (mp0) cc_final: 0.8771 (mp0) REVERT: G 124 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8861 (tppt) REVERT: G 150 MET cc_start: 0.8118 (tmm) cc_final: 0.7536 (tmm) REVERT: G 168 GLU cc_start: 0.8897 (mp0) cc_final: 0.8514 (pm20) REVERT: G 179 MET cc_start: 0.8601 (ptt) cc_final: 0.8248 (ptt) REVERT: G 254 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8246 (tm-30) REVERT: G 265 GLN cc_start: 0.9184 (mm110) cc_final: 0.8957 (mp10) REVERT: G 330 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9183 (pp) REVERT: G 337 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8068 (tp) REVERT: G 352 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8381 (tm-30) REVERT: G 395 GLU cc_start: 0.8483 (mp0) cc_final: 0.8226 (mp0) REVERT: O 1 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5151 (pmm) REVERT: H 15 ASP cc_start: 0.8432 (t0) cc_final: 0.8184 (t0) REVERT: H 37 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7848 (mm) REVERT: H 82 MET cc_start: 0.9314 (mmm) cc_final: 0.9055 (mmm) REVERT: H 98 GLU cc_start: 0.9063 (mp0) cc_final: 0.8784 (mp0) REVERT: H 128 ARG cc_start: 0.7834 (ptt-90) cc_final: 0.7462 (ptt-90) REVERT: H 150 MET cc_start: 0.8186 (tmm) cc_final: 0.7647 (tmm) REVERT: H 168 GLU cc_start: 0.8891 (mp0) cc_final: 0.8447 (pm20) REVERT: H 226 ASP cc_start: 0.9048 (m-30) cc_final: 0.8813 (m-30) REVERT: H 279 ASN cc_start: 0.7616 (t0) cc_final: 0.6570 (t0) REVERT: H 330 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9101 (pp) REVERT: H 337 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7764 (tp) REVERT: H 352 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8431 (tm-30) REVERT: H 395 GLU cc_start: 0.8457 (mp0) cc_final: 0.8186 (mp0) REVERT: H 505 SER cc_start: 0.8928 (t) cc_final: 0.8660 (t) REVERT: P 1 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.2925 (pp-130) outliers start: 199 outliers final: 110 residues processed: 1095 average time/residue: 0.4228 time to fit residues: 753.8416 Evaluate side-chains 1068 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 926 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain P residue 1 MET 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: 7.9990 chunk 74 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 379 optimal weight: 0.8980 chunk 314 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32352 Z= 0.288 Angle : 0.697 9.160 43936 Z= 0.337 Chirality : 0.048 0.166 5000 Planarity : 0.004 0.041 5456 Dihedral : 15.656 170.111 5358 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 7.40 % Allowed : 25.24 % Favored : 67.36 % 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: -1.46 (0.13), residues: 3968 helix: -0.43 (0.14), residues: 1280 sheet: -1.72 (0.24), residues: 448 loop : -1.09 (0.14), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 454 PHE 0.029 0.001 PHE B 401 TYR 0.014 0.001 TYR D 353 ARG 0.008 0.001 ARG G 105 *********************** 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 1142 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 900 time to evaluate : 2.924 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 15 ASP cc_start: 0.8722 (t0) cc_final: 0.8504 (t0) REVERT: A 59 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (pt) REVERT: A 124 LYS cc_start: 0.9180 (mmmt) cc_final: 0.8941 (tppt) REVERT: A 150 MET cc_start: 0.8325 (tmm) cc_final: 0.7744 (tmm) REVERT: A 168 GLU cc_start: 0.8976 (mp0) cc_final: 0.8553 (pm20) REVERT: A 179 MET cc_start: 0.8591 (ptt) cc_final: 0.8322 (ptm) REVERT: A 272 VAL cc_start: 0.8615 (t) cc_final: 0.8251 (p) REVERT: A 330 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9083 (pp) REVERT: A 337 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7962 (tp) REVERT: A 352 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8419 (tm-30) REVERT: I 1 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.2951 (pp-130) REVERT: B 15 ASP cc_start: 0.8523 (t0) cc_final: 0.8291 (t0) REVERT: B 59 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8595 (pt) REVERT: B 128 ARG cc_start: 0.7760 (ptt-90) cc_final: 0.7485 (ptt-90) REVERT: B 168 GLU cc_start: 0.8921 (mp0) cc_final: 0.8497 (pm20) REVERT: B 175 LEU cc_start: 0.9486 (mp) cc_final: 0.9280 (mp) REVERT: B 250 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8210 (pp) REVERT: B 330 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9157 (pp) REVERT: B 379 LEU cc_start: 0.9188 (mm) cc_final: 0.8837 (mt) REVERT: B 512 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.7786 (ttp80) REVERT: C 15 ASP cc_start: 0.8538 (t0) cc_final: 0.8218 (t70) REVERT: C 98 GLU cc_start: 0.9054 (mp0) cc_final: 0.8793 (mp0) REVERT: C 128 ARG cc_start: 0.8860 (mtm180) cc_final: 0.8500 (mtm-85) REVERT: C 168 GLU cc_start: 0.8906 (mp0) cc_final: 0.8459 (pm20) REVERT: C 205 LYS cc_start: 0.9125 (mptt) cc_final: 0.8824 (mmtm) REVERT: C 254 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8307 (tm-30) REVERT: C 272 VAL cc_start: 0.8641 (t) cc_final: 0.8270 (p) REVERT: C 330 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9132 (pp) REVERT: C 352 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8414 (tm-30) REVERT: C 512 ARG cc_start: 0.8478 (ttp-170) cc_final: 0.7900 (ttp80) REVERT: K 1 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.2812 (pp-130) REVERT: D 15 ASP cc_start: 0.8517 (t0) cc_final: 0.8293 (t0) REVERT: D 37 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7711 (mm) REVERT: D 51 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8727 (pp) REVERT: D 75 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7816 (mm-30) REVERT: D 78 MET cc_start: 0.8805 (ttp) cc_final: 0.8362 (ttp) REVERT: D 112 GLN cc_start: 0.7986 (mp10) cc_final: 0.6675 (mp10) REVERT: D 128 ARG cc_start: 0.7724 (ptt-90) cc_final: 0.7378 (ptt-90) REVERT: D 168 GLU cc_start: 0.8914 (mp0) cc_final: 0.8460 (pm20) REVERT: D 206 LYS cc_start: 0.8089 (mmpt) cc_final: 0.7861 (mmmt) REVERT: D 254 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8235 (tm-30) REVERT: D 330 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9167 (pp) REVERT: D 379 LEU cc_start: 0.9212 (mm) cc_final: 0.8919 (mt) REVERT: D 512 ARG cc_start: 0.8637 (mtp180) cc_final: 0.8303 (mtp85) REVERT: L 1 MET cc_start: 0.5874 (OUTLIER) cc_final: 0.2987 (pp-130) REVERT: E 78 MET cc_start: 0.8655 (ttp) cc_final: 0.8344 (tmm) REVERT: E 112 GLN cc_start: 0.8024 (mp10) cc_final: 0.6833 (mp10) REVERT: E 128 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8618 (mtm-85) REVERT: E 168 GLU cc_start: 0.8920 (mp0) cc_final: 0.8512 (pm20) REVERT: E 175 LEU cc_start: 0.9366 (mp) cc_final: 0.9134 (mp) REVERT: E 272 VAL cc_start: 0.8696 (t) cc_final: 0.8300 (p) REVERT: E 329 SER cc_start: 0.9405 (p) cc_final: 0.9162 (p) REVERT: E 330 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9098 (pp) REVERT: E 337 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7891 (tp) REVERT: E 352 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8462 (tm-30) REVERT: E 395 GLU cc_start: 0.8514 (mp0) cc_final: 0.8184 (mp0) REVERT: F 15 ASP cc_start: 0.8498 (t0) cc_final: 0.8262 (t0) REVERT: F 37 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7745 (mm) REVERT: F 59 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8764 (pt) REVERT: F 112 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7934 (mp10) REVERT: F 128 ARG cc_start: 0.7776 (ptt-90) cc_final: 0.7351 (ptt-90) REVERT: F 168 GLU cc_start: 0.8916 (mp0) cc_final: 0.8555 (pm20) REVERT: F 175 LEU cc_start: 0.9432 (mp) cc_final: 0.9203 (mp) REVERT: F 330 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9166 (pp) REVERT: F 395 GLU cc_start: 0.8423 (mp0) cc_final: 0.8151 (mp0) REVERT: F 470 ASP cc_start: 0.9057 (m-30) cc_final: 0.8808 (m-30) REVERT: F 505 SER cc_start: 0.9052 (t) cc_final: 0.8817 (p) REVERT: N 1 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.3105 (pp-130) REVERT: G 37 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8105 (mm) REVERT: G 59 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8726 (pt) REVERT: G 75 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7965 (mm-30) REVERT: G 78 MET cc_start: 0.8861 (ttp) cc_final: 0.8592 (ttp) REVERT: G 124 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8871 (tppt) REVERT: G 128 ARG cc_start: 0.8831 (mtm180) cc_final: 0.8479 (mtm-85) REVERT: G 150 MET cc_start: 0.8200 (tmm) cc_final: 0.7654 (tmm) REVERT: G 168 GLU cc_start: 0.8959 (mp0) cc_final: 0.8551 (pm20) REVERT: G 179 MET cc_start: 0.8521 (ptt) cc_final: 0.8281 (ptm) REVERT: G 265 GLN cc_start: 0.9220 (mm110) cc_final: 0.8982 (mp10) REVERT: G 272 VAL cc_start: 0.8580 (t) cc_final: 0.8256 (p) REVERT: G 330 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9131 (pp) REVERT: G 335 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7202 (mp0) REVERT: G 337 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8002 (tp) REVERT: G 352 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8441 (tm-30) REVERT: G 395 GLU cc_start: 0.8520 (mp0) cc_final: 0.8146 (mp0) REVERT: O 1 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5112 (pmm) REVERT: H 15 ASP cc_start: 0.8521 (t0) cc_final: 0.8315 (t0) REVERT: H 37 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7747 (mm) REVERT: H 98 GLU cc_start: 0.9103 (mp0) cc_final: 0.8756 (mp0) REVERT: H 128 ARG cc_start: 0.7746 (ptt-90) cc_final: 0.7437 (ptt-90) REVERT: H 136 ARG cc_start: 0.9079 (ttm110) cc_final: 0.8840 (mtp-110) REVERT: H 150 MET cc_start: 0.8255 (tmm) cc_final: 0.7643 (tmm) REVERT: H 168 GLU cc_start: 0.8947 (mp0) cc_final: 0.8509 (pm20) REVERT: H 216 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8686 (t0) REVERT: H 330 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9133 (pp) REVERT: H 335 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7237 (mp0) REVERT: H 337 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7894 (tp) REVERT: H 395 GLU cc_start: 0.8439 (mp0) cc_final: 0.8179 (mp0) REVERT: H 470 ASP cc_start: 0.8867 (m-30) cc_final: 0.8637 (m-30) REVERT: H 505 SER cc_start: 0.9025 (t) cc_final: 0.8781 (t) REVERT: P 1 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.2894 (pp-130) outliers start: 242 outliers final: 153 residues processed: 1035 average time/residue: 0.4540 time to fit residues: 774.0083 Evaluate side-chains 1054 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 872 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 467 SER Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 216 optimal weight: 0.0670 chunk 276 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 319 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 377 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 230 optimal weight: 0.4980 chunk 174 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 100 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32352 Z= 0.187 Angle : 0.668 9.403 43936 Z= 0.316 Chirality : 0.046 0.165 5000 Planarity : 0.004 0.034 5456 Dihedral : 15.312 169.517 5358 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 6.39 % Allowed : 26.31 % Favored : 67.30 % 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: -1.38 (0.13), residues: 3968 helix: -0.28 (0.14), residues: 1280 sheet: -1.60 (0.23), residues: 488 loop : -1.09 (0.14), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 466 PHE 0.019 0.001 PHE D 401 TYR 0.013 0.001 TYR D 353 ARG 0.007 0.001 ARG D 105 *********************** 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 1133 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 924 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8579 (t0) cc_final: 0.8353 (t0) REVERT: A 59 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8609 (pt) REVERT: A 75 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8058 (mm-30) REVERT: A 94 ASN cc_start: 0.8492 (t0) cc_final: 0.8288 (t0) REVERT: A 124 LYS cc_start: 0.9183 (mmmt) cc_final: 0.8912 (tppt) REVERT: A 150 MET cc_start: 0.8307 (tmm) cc_final: 0.7757 (tmm) REVERT: A 168 GLU cc_start: 0.8941 (mp0) cc_final: 0.8506 (pm20) REVERT: A 216 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8724 (t0) REVERT: A 258 TYR cc_start: 0.8882 (t80) cc_final: 0.8526 (t80) REVERT: A 330 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9112 (pp) REVERT: A 337 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8059 (tp) REVERT: A 352 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8400 (tm-30) REVERT: I 1 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.2892 (pp-130) REVERT: B 15 ASP cc_start: 0.8496 (t0) cc_final: 0.8289 (t0) REVERT: B 59 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8536 (pt) REVERT: B 128 ARG cc_start: 0.7794 (ptt-90) cc_final: 0.7437 (ptt-90) REVERT: B 168 GLU cc_start: 0.8916 (mp0) cc_final: 0.8581 (pm20) REVERT: B 175 LEU cc_start: 0.9364 (mp) cc_final: 0.9149 (mp) REVERT: B 224 ARG cc_start: 0.8766 (ttt90) cc_final: 0.8343 (ttt90) REVERT: B 330 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9166 (pp) REVERT: B 343 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: B 512 ARG cc_start: 0.8411 (ttp-170) cc_final: 0.7844 (ttp80) REVERT: C 75 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8013 (mm-30) REVERT: C 98 GLU cc_start: 0.9041 (mp0) cc_final: 0.8770 (mp0) REVERT: C 128 ARG cc_start: 0.8867 (mtm180) cc_final: 0.8503 (mtm-85) REVERT: C 150 MET cc_start: 0.8209 (tmm) cc_final: 0.7981 (tmm) REVERT: C 168 GLU cc_start: 0.8896 (mp0) cc_final: 0.8451 (pm20) REVERT: C 205 LYS cc_start: 0.9010 (mptt) cc_final: 0.8805 (mptt) REVERT: C 254 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8268 (tm-30) REVERT: C 272 VAL cc_start: 0.8585 (t) cc_final: 0.8175 (p) REVERT: C 330 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9192 (pp) REVERT: C 335 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7229 (mp0) REVERT: C 337 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7719 (tp) REVERT: C 352 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8368 (tm-30) REVERT: K 1 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.2848 (pp-130) REVERT: D 15 ASP cc_start: 0.8518 (t0) cc_final: 0.8293 (t0) REVERT: D 37 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7489 (mm) REVERT: D 51 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8513 (pp) REVERT: D 75 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7880 (mm-30) REVERT: D 78 MET cc_start: 0.8820 (ttp) cc_final: 0.8406 (ttp) REVERT: D 98 GLU cc_start: 0.9035 (mp0) cc_final: 0.8705 (mp0) REVERT: D 128 ARG cc_start: 0.7685 (ptt-90) cc_final: 0.7339 (ptt-90) REVERT: D 150 MET cc_start: 0.8095 (tmm) cc_final: 0.7548 (tmm) REVERT: D 168 GLU cc_start: 0.8920 (mp0) cc_final: 0.8487 (pm20) REVERT: D 206 LYS cc_start: 0.8190 (mmpt) cc_final: 0.7896 (mmmt) REVERT: D 216 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8630 (t0) REVERT: D 330 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9053 (pp) REVERT: D 379 LEU cc_start: 0.9175 (mm) cc_final: 0.8772 (mt) REVERT: D 512 ARG cc_start: 0.8470 (mtp180) cc_final: 0.8203 (mmm160) REVERT: L 1 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.3063 (pp-130) REVERT: E 112 GLN cc_start: 0.8213 (mp10) cc_final: 0.6755 (mp10) REVERT: E 128 ARG cc_start: 0.8830 (mtm180) cc_final: 0.8614 (mtm-85) REVERT: E 168 GLU cc_start: 0.8908 (mp0) cc_final: 0.8535 (pm20) REVERT: E 175 LEU cc_start: 0.9400 (mp) cc_final: 0.9181 (mp) REVERT: E 272 VAL cc_start: 0.8585 (t) cc_final: 0.8165 (p) REVERT: E 274 ASP cc_start: 0.8743 (t0) cc_final: 0.8490 (t0) REVERT: E 330 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9194 (pp) REVERT: E 335 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7194 (mp0) REVERT: E 337 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7922 (tp) REVERT: E 352 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8402 (tm-30) REVERT: E 395 GLU cc_start: 0.8516 (mp0) cc_final: 0.8192 (mp0) REVERT: E 471 ILE cc_start: 0.8111 (mm) cc_final: 0.7867 (mm) REVERT: F 15 ASP cc_start: 0.8504 (t0) cc_final: 0.8288 (t0) REVERT: F 37 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7785 (mm) REVERT: F 51 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8739 (pp) REVERT: F 59 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8709 (pt) REVERT: F 128 ARG cc_start: 0.7742 (ptt-90) cc_final: 0.7325 (ptt-90) REVERT: F 150 MET cc_start: 0.8174 (tmm) cc_final: 0.7617 (tmm) REVERT: F 168 GLU cc_start: 0.8969 (mp0) cc_final: 0.8527 (pm20) REVERT: F 175 LEU cc_start: 0.9386 (mp) cc_final: 0.9127 (mp) REVERT: F 330 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9196 (pp) REVERT: F 395 GLU cc_start: 0.8449 (mp0) cc_final: 0.8175 (mp0) REVERT: F 414 MET cc_start: 0.8703 (mmm) cc_final: 0.8452 (mmm) REVERT: F 505 SER cc_start: 0.9038 (t) cc_final: 0.8787 (t) REVERT: N 1 MET cc_start: 0.5966 (OUTLIER) cc_final: 0.3007 (pp-130) REVERT: G 59 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8671 (pt) REVERT: G 75 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8034 (mm-30) REVERT: G 78 MET cc_start: 0.8884 (ttp) cc_final: 0.8540 (ttp) REVERT: G 94 ASN cc_start: 0.8562 (t0) cc_final: 0.8344 (t0) REVERT: G 124 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8839 (tppt) REVERT: G 128 ARG cc_start: 0.8771 (mtm180) cc_final: 0.8421 (mtm-85) REVERT: G 150 MET cc_start: 0.8118 (tmm) cc_final: 0.7601 (tmm) REVERT: G 168 GLU cc_start: 0.8946 (mp0) cc_final: 0.8580 (pm20) REVERT: G 272 VAL cc_start: 0.8563 (t) cc_final: 0.8201 (p) REVERT: G 330 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9173 (pp) REVERT: G 335 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7196 (mp0) REVERT: G 337 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8080 (tp) REVERT: G 352 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8383 (tm-30) REVERT: G 395 GLU cc_start: 0.8482 (mp0) cc_final: 0.8130 (mp0) REVERT: O 1 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.4904 (pmm) REVERT: H 15 ASP cc_start: 0.8514 (t0) cc_final: 0.8300 (t0) REVERT: H 37 ILE cc_start: 0.7874 (mm) cc_final: 0.7654 (mm) REVERT: H 98 GLU cc_start: 0.9091 (mp0) cc_final: 0.8817 (mp0) REVERT: H 128 ARG cc_start: 0.7739 (ptt-90) cc_final: 0.7419 (ptt-90) REVERT: H 136 ARG cc_start: 0.9106 (ttm110) cc_final: 0.8871 (mtp-110) REVERT: H 150 MET cc_start: 0.8333 (tmm) cc_final: 0.7828 (tmm) REVERT: H 168 GLU cc_start: 0.8925 (mp0) cc_final: 0.8608 (pm20) REVERT: H 216 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8626 (t0) REVERT: H 254 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8147 (tm-30) REVERT: H 330 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9174 (pp) REVERT: H 337 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7621 (tp) REVERT: H 352 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8270 (tm-30) REVERT: H 395 GLU cc_start: 0.8445 (mp0) cc_final: 0.8175 (mp0) REVERT: H 470 ASP cc_start: 0.8847 (m-30) cc_final: 0.8645 (m-30) REVERT: H 505 SER cc_start: 0.9008 (t) cc_final: 0.8749 (t) REVERT: P 1 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.3183 (pp-130) outliers start: 209 outliers final: 138 residues processed: 1040 average time/residue: 0.4205 time to fit residues: 710.3756 Evaluate side-chains 1047 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 878 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 225 optimal weight: 0.0970 chunk 113 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 240 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 296 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32352 Z= 0.187 Angle : 0.671 9.519 43936 Z= 0.317 Chirality : 0.046 0.189 5000 Planarity : 0.004 0.056 5456 Dihedral : 15.020 170.323 5358 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 6.39 % Allowed : 26.59 % Favored : 67.02 % 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: -1.31 (0.13), residues: 3968 helix: -0.27 (0.14), residues: 1296 sheet: -1.59 (0.23), residues: 488 loop : -1.02 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 466 PHE 0.017 0.001 PHE H 165 TYR 0.011 0.001 TYR E 353 ARG 0.009 0.001 ARG E 105 *********************** 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 1115 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 906 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8564 (t0) cc_final: 0.8351 (t0) REVERT: A 59 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8514 (pt) REVERT: A 75 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8030 (mm-30) REVERT: A 94 ASN cc_start: 0.8596 (t0) cc_final: 0.8377 (t0) REVERT: A 109 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8191 (mmtm) REVERT: A 112 GLN cc_start: 0.7932 (mp10) cc_final: 0.6581 (mp10) REVERT: A 124 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8855 (tppt) REVERT: A 150 MET cc_start: 0.8270 (tmm) cc_final: 0.7722 (tmm) REVERT: A 168 GLU cc_start: 0.8957 (mp0) cc_final: 0.8632 (pm20) REVERT: A 216 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8708 (t0) REVERT: A 258 TYR cc_start: 0.8837 (t80) cc_final: 0.8426 (t80) REVERT: A 330 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9104 (pp) REVERT: A 337 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8099 (tp) REVERT: A 352 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 469 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8539 (tt0) REVERT: I 1 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.3085 (pp-130) REVERT: B 59 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8467 (pt) REVERT: B 75 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7785 (mm-30) REVERT: B 128 ARG cc_start: 0.7740 (ptt-90) cc_final: 0.7420 (ptt-90) REVERT: B 150 MET cc_start: 0.8189 (tmm) cc_final: 0.7633 (tmm) REVERT: B 168 GLU cc_start: 0.8975 (mp0) cc_final: 0.8549 (pm20) REVERT: B 199 GLU cc_start: 0.9141 (pt0) cc_final: 0.8737 (pt0) REVERT: B 224 ARG cc_start: 0.8705 (ttt90) cc_final: 0.8179 (ttt90) REVERT: B 330 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9109 (pp) REVERT: B 343 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: B 411 TYR cc_start: 0.8754 (t80) cc_final: 0.8416 (t80) REVERT: B 512 ARG cc_start: 0.8463 (ttp-170) cc_final: 0.7825 (ttp80) REVERT: C 51 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8818 (pp) REVERT: C 98 GLU cc_start: 0.9033 (mp0) cc_final: 0.8790 (mp0) REVERT: C 128 ARG cc_start: 0.8911 (mtm180) cc_final: 0.8525 (mtm-85) REVERT: C 150 MET cc_start: 0.8108 (tmm) cc_final: 0.7883 (tmm) REVERT: C 168 GLU cc_start: 0.8911 (mp0) cc_final: 0.8509 (pm20) REVERT: C 205 LYS cc_start: 0.8987 (mptt) cc_final: 0.8764 (mptt) REVERT: C 272 VAL cc_start: 0.8633 (t) cc_final: 0.8223 (p) REVERT: C 330 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9124 (pp) REVERT: C 335 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7228 (mp0) REVERT: C 337 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7746 (tp) REVERT: C 352 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8345 (tm-30) REVERT: C 395 GLU cc_start: 0.8526 (mp0) cc_final: 0.8227 (mp0) REVERT: C 512 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8151 (ttp80) REVERT: K 1 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.3166 (pp-130) REVERT: D 15 ASP cc_start: 0.8505 (t0) cc_final: 0.8297 (t0) REVERT: D 51 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8409 (pp) REVERT: D 75 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7909 (mm-30) REVERT: D 98 GLU cc_start: 0.9009 (mp0) cc_final: 0.8703 (mp0) REVERT: D 128 ARG cc_start: 0.7669 (ptt-90) cc_final: 0.7305 (ptt-90) REVERT: D 150 MET cc_start: 0.8127 (tmm) cc_final: 0.7599 (tmm) REVERT: D 168 GLU cc_start: 0.8929 (mp0) cc_final: 0.8521 (pm20) REVERT: D 206 LYS cc_start: 0.8194 (mmpt) cc_final: 0.7913 (mmmt) REVERT: D 216 ASP cc_start: 0.9125 (OUTLIER) cc_final: 0.8643 (t0) REVERT: D 254 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8350 (tm-30) REVERT: D 330 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9145 (pp) REVERT: D 512 ARG cc_start: 0.8518 (mtp180) cc_final: 0.8229 (mmm160) REVERT: L 1 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.2846 (pp-130) REVERT: E 51 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8795 (pp) REVERT: E 128 ARG cc_start: 0.8810 (mtm180) cc_final: 0.8588 (mtm-85) REVERT: E 168 GLU cc_start: 0.8928 (mp0) cc_final: 0.8508 (pm20) REVERT: E 254 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8290 (tm-30) REVERT: E 272 VAL cc_start: 0.8548 (t) cc_final: 0.8123 (p) REVERT: E 274 ASP cc_start: 0.8710 (t0) cc_final: 0.8438 (t0) REVERT: E 325 MET cc_start: 0.8319 (ttm) cc_final: 0.8069 (ttt) REVERT: E 329 SER cc_start: 0.9381 (p) cc_final: 0.9177 (p) REVERT: E 330 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9173 (pp) REVERT: E 335 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7201 (mp0) REVERT: E 337 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7909 (tp) REVERT: E 352 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8401 (tm-30) REVERT: E 395 GLU cc_start: 0.8466 (mp0) cc_final: 0.8195 (mp0) REVERT: E 469 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8581 (tt0) REVERT: F 15 ASP cc_start: 0.8491 (t0) cc_final: 0.8289 (t0) REVERT: F 37 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7788 (mm) REVERT: F 51 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8430 (pp) REVERT: F 128 ARG cc_start: 0.7725 (ptt-90) cc_final: 0.7303 (ptt-90) REVERT: F 150 MET cc_start: 0.8202 (tmm) cc_final: 0.7694 (tmm) REVERT: F 168 GLU cc_start: 0.8991 (mp0) cc_final: 0.8563 (pm20) REVERT: F 175 LEU cc_start: 0.9411 (mp) cc_final: 0.9188 (mt) REVERT: F 330 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9197 (pp) REVERT: F 395 GLU cc_start: 0.8465 (mp0) cc_final: 0.8140 (mp0) REVERT: F 414 MET cc_start: 0.8689 (mmm) cc_final: 0.8388 (mmm) REVERT: F 469 GLN cc_start: 0.9267 (tm-30) cc_final: 0.9047 (tt0) REVERT: F 505 SER cc_start: 0.9041 (t) cc_final: 0.8787 (t) REVERT: N 1 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.3359 (pp-130) REVERT: G 59 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8605 (pt) REVERT: G 75 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8051 (mm-30) REVERT: G 78 MET cc_start: 0.8886 (ttp) cc_final: 0.8644 (ttp) REVERT: G 94 ASN cc_start: 0.8650 (t0) cc_final: 0.8398 (t0) REVERT: G 98 GLU cc_start: 0.8962 (mp0) cc_final: 0.8728 (mp0) REVERT: G 124 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8849 (tppt) REVERT: G 128 ARG cc_start: 0.8776 (mtm180) cc_final: 0.8439 (mtm-85) REVERT: G 150 MET cc_start: 0.8063 (tmm) cc_final: 0.7550 (tmm) REVERT: G 168 GLU cc_start: 0.8955 (mp0) cc_final: 0.8610 (pm20) REVERT: G 198 ASN cc_start: 0.9296 (m-40) cc_final: 0.8947 (m-40) REVERT: G 272 VAL cc_start: 0.8517 (t) cc_final: 0.8154 (p) REVERT: G 330 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9168 (pp) REVERT: G 335 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7166 (mp0) REVERT: G 337 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8014 (tp) REVERT: G 352 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8382 (tm-30) REVERT: O 1 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.5033 (pmm) REVERT: H 37 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7645 (mm) REVERT: H 51 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8359 (pp) REVERT: H 75 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7807 (mm-30) REVERT: H 128 ARG cc_start: 0.7689 (ptt-90) cc_final: 0.7354 (ptt-90) REVERT: H 136 ARG cc_start: 0.9125 (ttm110) cc_final: 0.8888 (mtp-110) REVERT: H 168 GLU cc_start: 0.9013 (mp0) cc_final: 0.8572 (pm20) REVERT: H 216 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8639 (t0) REVERT: H 330 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9176 (pp) REVERT: H 352 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8306 (tm-30) REVERT: H 395 GLU cc_start: 0.8446 (mp0) cc_final: 0.8146 (mp0) REVERT: H 469 GLN cc_start: 0.9250 (tm-30) cc_final: 0.9049 (tt0) REVERT: H 505 SER cc_start: 0.8999 (t) cc_final: 0.8759 (t) REVERT: P 1 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.3094 (pp-130) outliers start: 209 outliers final: 134 residues processed: 1025 average time/residue: 0.4291 time to fit residues: 715.6947 Evaluate side-chains 1037 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 871 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain P residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 5.9990 chunk 361 optimal weight: 0.0570 chunk 330 optimal weight: 1.9990 chunk 352 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 153 optimal weight: 0.0770 chunk 276 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 318 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 350 optimal weight: 4.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32352 Z= 0.225 Angle : 0.687 9.763 43936 Z= 0.327 Chirality : 0.047 0.182 5000 Planarity : 0.004 0.058 5456 Dihedral : 14.975 170.828 5358 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 6.05 % Allowed : 27.81 % Favored : 66.14 % 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: -1.24 (0.13), residues: 3968 helix: -0.22 (0.14), residues: 1296 sheet: -1.56 (0.23), residues: 488 loop : -0.97 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 171 PHE 0.025 0.001 PHE B 401 TYR 0.013 0.001 TYR C 400 ARG 0.010 0.001 ARG H 105 *********************** 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 1087 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 889 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8601 (t0) cc_final: 0.8331 (t0) REVERT: A 124 LYS cc_start: 0.9180 (mmmt) cc_final: 0.8900 (tppt) REVERT: A 150 MET cc_start: 0.8228 (tmm) cc_final: 0.7690 (tmm) REVERT: A 168 GLU cc_start: 0.8940 (mp0) cc_final: 0.8614 (pm20) REVERT: A 216 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8689 (t0) REVERT: A 258 TYR cc_start: 0.8875 (t80) cc_final: 0.8465 (t80) REVERT: A 272 VAL cc_start: 0.8514 (t) cc_final: 0.8206 (p) REVERT: A 330 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9117 (pp) REVERT: A 335 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7245 (mp0) REVERT: A 337 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8114 (tp) REVERT: A 352 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8436 (tm-30) REVERT: A 414 MET cc_start: 0.8704 (mmm) cc_final: 0.8501 (mmm) REVERT: I 1 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.2920 (pp-130) REVERT: B 59 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8480 (pt) REVERT: B 75 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7886 (mm-30) REVERT: B 128 ARG cc_start: 0.7694 (ptt-90) cc_final: 0.7373 (ptt-90) REVERT: B 150 MET cc_start: 0.8160 (tmm) cc_final: 0.7656 (tmm) REVERT: B 168 GLU cc_start: 0.9019 (mp0) cc_final: 0.8580 (pm20) REVERT: B 199 GLU cc_start: 0.9172 (pt0) cc_final: 0.8767 (pt0) REVERT: B 224 ARG cc_start: 0.8718 (ttt90) cc_final: 0.8307 (ttt90) REVERT: B 330 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9121 (pp) REVERT: B 343 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: B 512 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.7880 (ttp80) REVERT: C 51 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8849 (pp) REVERT: C 98 GLU cc_start: 0.9020 (mp0) cc_final: 0.8799 (mp0) REVERT: C 128 ARG cc_start: 0.8913 (mtm180) cc_final: 0.8522 (mtm-85) REVERT: C 150 MET cc_start: 0.8112 (tmm) cc_final: 0.7550 (tmm) REVERT: C 168 GLU cc_start: 0.8923 (mp0) cc_final: 0.8531 (pm20) REVERT: C 205 LYS cc_start: 0.8967 (mptt) cc_final: 0.8737 (mptt) REVERT: C 272 VAL cc_start: 0.8655 (t) cc_final: 0.8311 (p) REVERT: C 330 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9074 (pp) REVERT: C 335 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7274 (mp0) REVERT: C 337 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7876 (tp) REVERT: C 352 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8381 (tm-30) REVERT: C 379 LEU cc_start: 0.9165 (mt) cc_final: 0.8893 (mt) REVERT: C 395 GLU cc_start: 0.8492 (mp0) cc_final: 0.8171 (mp0) REVERT: C 512 ARG cc_start: 0.8478 (ttp80) cc_final: 0.8133 (ttp80) REVERT: K 1 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.2980 (pp-130) REVERT: D 51 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8506 (pp) REVERT: D 75 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7877 (mm-30) REVERT: D 78 MET cc_start: 0.8696 (ttp) cc_final: 0.8411 (ttp) REVERT: D 94 ASN cc_start: 0.8481 (t0) cc_final: 0.8272 (t0) REVERT: D 98 GLU cc_start: 0.9032 (mp0) cc_final: 0.8741 (mp0) REVERT: D 128 ARG cc_start: 0.7638 (ptt-90) cc_final: 0.7289 (ptt-90) REVERT: D 150 MET cc_start: 0.8126 (tmm) cc_final: 0.7639 (tmm) REVERT: D 168 GLU cc_start: 0.8944 (mp0) cc_final: 0.8542 (pm20) REVERT: D 206 LYS cc_start: 0.8204 (mmpt) cc_final: 0.7938 (mmmt) REVERT: D 216 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8640 (t0) REVERT: D 330 ILE cc_start: 0.9458 (OUTLIER) cc_final: 0.9162 (pp) REVERT: D 512 ARG cc_start: 0.8554 (mtp180) cc_final: 0.8249 (mmm160) REVERT: L 1 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.2899 (pp-130) REVERT: E 51 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8803 (pp) REVERT: E 124 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8783 (tppt) REVERT: E 128 ARG cc_start: 0.8823 (mtm180) cc_final: 0.8595 (mtm-85) REVERT: E 168 GLU cc_start: 0.8949 (mp0) cc_final: 0.8532 (pm20) REVERT: E 258 TYR cc_start: 0.8894 (t80) cc_final: 0.8438 (t80) REVERT: E 272 VAL cc_start: 0.8565 (t) cc_final: 0.8203 (p) REVERT: E 329 SER cc_start: 0.9387 (p) cc_final: 0.9146 (p) REVERT: E 330 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9140 (pp) REVERT: E 335 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7181 (mp0) REVERT: E 337 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7933 (tp) REVERT: E 352 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8416 (tm-30) REVERT: E 395 GLU cc_start: 0.8450 (mp0) cc_final: 0.8067 (mp0) REVERT: F 37 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7845 (mm) REVERT: F 51 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8475 (pp) REVERT: F 128 ARG cc_start: 0.7688 (ptt-90) cc_final: 0.7288 (ptt-90) REVERT: F 150 MET cc_start: 0.8192 (tmm) cc_final: 0.7700 (tmm) REVERT: F 168 GLU cc_start: 0.9009 (mp0) cc_final: 0.8592 (pm20) REVERT: F 175 LEU cc_start: 0.9363 (mp) cc_final: 0.9090 (mp) REVERT: F 254 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8299 (tm-30) REVERT: F 330 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9196 (pp) REVERT: F 395 GLU cc_start: 0.8468 (mp0) cc_final: 0.8160 (mp0) REVERT: F 414 MET cc_start: 0.8660 (mmm) cc_final: 0.8359 (mmm) REVERT: F 465 GLN cc_start: 0.8701 (pt0) cc_final: 0.8117 (mt0) REVERT: F 505 SER cc_start: 0.9071 (t) cc_final: 0.8824 (t) REVERT: N 1 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.3027 (pp-130) REVERT: G 51 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8868 (pp) REVERT: G 75 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8034 (mm-30) REVERT: G 78 MET cc_start: 0.8936 (ttp) cc_final: 0.8618 (ttp) REVERT: G 94 ASN cc_start: 0.8672 (t0) cc_final: 0.8428 (t0) REVERT: G 98 GLU cc_start: 0.8988 (mp0) cc_final: 0.8750 (mp0) REVERT: G 124 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8852 (tppt) REVERT: G 128 ARG cc_start: 0.8786 (mtm180) cc_final: 0.8452 (mtm-85) REVERT: G 150 MET cc_start: 0.8092 (tmm) cc_final: 0.7570 (tmm) REVERT: G 168 GLU cc_start: 0.8956 (mp0) cc_final: 0.8604 (pm20) REVERT: G 272 VAL cc_start: 0.8514 (t) cc_final: 0.8208 (p) REVERT: G 330 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9157 (pp) REVERT: G 335 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7170 (mp0) REVERT: G 337 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7993 (tp) REVERT: G 352 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8398 (tm-30) REVERT: O 1 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.5005 (pmm) REVERT: H 37 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7752 (mm) REVERT: H 51 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8470 (pp) REVERT: H 75 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7821 (mm-30) REVERT: H 128 ARG cc_start: 0.7699 (ptt-90) cc_final: 0.7377 (ptt-90) REVERT: H 136 ARG cc_start: 0.9134 (ttm110) cc_final: 0.8895 (mtp-110) REVERT: H 150 MET cc_start: 0.8125 (tmm) cc_final: 0.7561 (tmm) REVERT: H 168 GLU cc_start: 0.9035 (mp0) cc_final: 0.8607 (pm20) REVERT: H 216 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8644 (t0) REVERT: H 330 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9175 (pp) REVERT: H 395 GLU cc_start: 0.8480 (mp0) cc_final: 0.8161 (mp0) REVERT: H 414 MET cc_start: 0.8648 (mmm) cc_final: 0.8423 (mmm) REVERT: H 469 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8508 (tt0) REVERT: H 505 SER cc_start: 0.9018 (t) cc_final: 0.8793 (t) REVERT: P 1 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.3006 (pp-130) outliers start: 198 outliers final: 144 residues processed: 996 average time/residue: 0.4134 time to fit residues: 671.3160 Evaluate side-chains 1038 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 863 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain P residue 1 MET 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: 0.6980 chunk 227 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 258 optimal weight: 0.0870 chunk 390 optimal weight: 4.9990 chunk 359 optimal weight: 9.9990 chunk 310 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 240 optimal weight: 0.0030 chunk 190 optimal weight: 0.7980 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN E 309 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32352 Z= 0.166 Angle : 0.676 10.061 43936 Z= 0.318 Chirality : 0.046 0.176 5000 Planarity : 0.004 0.051 5456 Dihedral : 14.538 170.945 5358 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.98 % Allowed : 28.94 % Favored : 66.08 % 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: -1.20 (0.13), residues: 3968 helix: -0.07 (0.14), residues: 1272 sheet: -1.60 (0.23), residues: 488 loop : -0.99 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 466 PHE 0.032 0.001 PHE F 401 TYR 0.011 0.001 TYR A 110 ARG 0.010 0.001 ARG A 105 ********************** 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 1102 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 939 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8571 (t0) cc_final: 0.8313 (t70) REVERT: A 51 LEU cc_start: 0.9048 (pp) cc_final: 0.8657 (pp) REVERT: A 124 LYS cc_start: 0.9187 (mmmt) cc_final: 0.8886 (tppt) REVERT: A 150 MET cc_start: 0.8129 (tmm) cc_final: 0.7621 (tmm) REVERT: A 168 GLU cc_start: 0.8889 (mp0) cc_final: 0.8564 (pm20) REVERT: A 258 TYR cc_start: 0.8728 (t80) cc_final: 0.8280 (t80) REVERT: A 330 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9125 (pp) REVERT: A 337 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8090 (tp) REVERT: A 352 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8406 (tm-30) REVERT: A 469 GLN cc_start: 0.9250 (tm-30) cc_final: 0.8599 (tt0) REVERT: I 1 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.3077 (pp-130) REVERT: B 51 LEU cc_start: 0.8947 (pp) cc_final: 0.8741 (pp) REVERT: B 75 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7848 (mm-30) REVERT: B 128 ARG cc_start: 0.7690 (ptt-90) cc_final: 0.7461 (ptt-90) REVERT: B 150 MET cc_start: 0.8119 (tmm) cc_final: 0.7589 (tmm) REVERT: B 168 GLU cc_start: 0.9011 (mp0) cc_final: 0.8611 (pm20) REVERT: B 199 GLU cc_start: 0.9153 (pt0) cc_final: 0.8754 (pt0) REVERT: B 224 ARG cc_start: 0.8578 (ttt90) cc_final: 0.8109 (ttt90) REVERT: B 330 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9009 (pp) REVERT: B 343 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: B 469 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8574 (tt0) REVERT: B 512 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.7857 (ttp80) REVERT: C 51 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8716 (pp) REVERT: C 94 ASN cc_start: 0.8656 (t0) cc_final: 0.8405 (t0) REVERT: C 98 GLU cc_start: 0.9042 (mp0) cc_final: 0.8678 (mp0) REVERT: C 128 ARG cc_start: 0.8916 (mtm180) cc_final: 0.8514 (mtm-85) REVERT: C 150 MET cc_start: 0.8055 (tmm) cc_final: 0.7480 (tmm) REVERT: C 168 GLU cc_start: 0.8918 (mp0) cc_final: 0.8551 (pm20) REVERT: C 258 TYR cc_start: 0.8696 (t80) cc_final: 0.8263 (t80) REVERT: C 272 VAL cc_start: 0.8651 (t) cc_final: 0.8241 (p) REVERT: C 330 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9071 (pp) REVERT: C 335 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7200 (mp0) REVERT: C 337 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7904 (tp) REVERT: C 352 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8316 (tm-30) REVERT: C 395 GLU cc_start: 0.8634 (mp0) cc_final: 0.8375 (mp0) REVERT: C 465 GLN cc_start: 0.8444 (pt0) cc_final: 0.7904 (mt0) REVERT: C 469 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8655 (tt0) REVERT: C 512 ARG cc_start: 0.8513 (ttp80) cc_final: 0.8130 (ttp80) REVERT: K 1 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.3079 (pp-130) REVERT: D 51 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8222 (pp) REVERT: D 98 GLU cc_start: 0.9008 (mp0) cc_final: 0.8733 (mp0) REVERT: D 128 ARG cc_start: 0.7680 (ptt-90) cc_final: 0.7342 (ptt-90) REVERT: D 150 MET cc_start: 0.8111 (tmm) cc_final: 0.7642 (tmm) REVERT: D 168 GLU cc_start: 0.8929 (mp0) cc_final: 0.8555 (pm20) REVERT: D 206 LYS cc_start: 0.8205 (mmpt) cc_final: 0.7916 (mmmt) REVERT: D 216 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8611 (t0) REVERT: D 224 ARG cc_start: 0.8646 (ptm160) cc_final: 0.8396 (ptm160) REVERT: D 330 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9096 (pp) REVERT: D 411 TYR cc_start: 0.8605 (t80) cc_final: 0.8380 (t80) REVERT: D 465 GLN cc_start: 0.8536 (pt0) cc_final: 0.8137 (mt0) REVERT: D 512 ARG cc_start: 0.8509 (mtp180) cc_final: 0.8008 (mmm160) REVERT: L 1 MET cc_start: 0.5756 (OUTLIER) cc_final: 0.2894 (pp-130) REVERT: E 51 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8703 (pp) REVERT: E 128 ARG cc_start: 0.8827 (mtm180) cc_final: 0.8603 (mtm-85) REVERT: E 168 GLU cc_start: 0.8936 (mp0) cc_final: 0.8568 (pm20) REVERT: E 258 TYR cc_start: 0.8829 (t80) cc_final: 0.8472 (t80) REVERT: E 274 ASP cc_start: 0.8670 (t0) cc_final: 0.8394 (t0) REVERT: E 330 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9234 (pp) REVERT: E 335 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7091 (mp0) REVERT: E 337 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7947 (tp) REVERT: E 352 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8426 (tm-30) REVERT: E 469 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8619 (tt0) REVERT: F 37 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7712 (mm) REVERT: F 51 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8395 (pp) REVERT: F 105 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8294 (ttp-110) REVERT: F 128 ARG cc_start: 0.7697 (ptt-90) cc_final: 0.7370 (ptt-90) REVERT: F 150 MET cc_start: 0.8096 (tmm) cc_final: 0.7636 (tmm) REVERT: F 168 GLU cc_start: 0.9002 (mp0) cc_final: 0.8605 (pm20) REVERT: F 185 LEU cc_start: 0.9080 (mt) cc_final: 0.8822 (mt) REVERT: F 330 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9207 (pp) REVERT: F 395 GLU cc_start: 0.8406 (mp0) cc_final: 0.8035 (mp0) REVERT: F 414 MET cc_start: 0.8666 (mmm) cc_final: 0.8264 (mmm) REVERT: F 505 SER cc_start: 0.9034 (t) cc_final: 0.8783 (t) REVERT: N 1 MET cc_start: 0.5947 (OUTLIER) cc_final: 0.3085 (pp-130) REVERT: G 59 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8504 (pt) REVERT: G 78 MET cc_start: 0.8885 (ttp) cc_final: 0.8293 (tmm) REVERT: G 124 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8825 (tppt) REVERT: G 128 ARG cc_start: 0.8798 (mtm180) cc_final: 0.8461 (mtm-85) REVERT: G 150 MET cc_start: 0.8012 (tmm) cc_final: 0.7490 (tmm) REVERT: G 168 GLU cc_start: 0.8972 (mp0) cc_final: 0.8614 (pm20) REVERT: G 224 ARG cc_start: 0.8480 (ttt90) cc_final: 0.7988 (ttt90) REVERT: G 272 VAL cc_start: 0.8355 (t) cc_final: 0.8027 (p) REVERT: G 330 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9199 (pp) REVERT: G 337 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8063 (tp) REVERT: G 352 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8364 (tm-30) REVERT: G 393 THR cc_start: 0.7660 (p) cc_final: 0.7273 (t) REVERT: G 469 GLN cc_start: 0.9249 (tm-30) cc_final: 0.8556 (tt0) REVERT: O 1 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.4937 (pmm) REVERT: H 37 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7660 (mm) REVERT: H 51 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8276 (pp) REVERT: H 136 ARG cc_start: 0.9088 (ttm110) cc_final: 0.8838 (mtp-110) REVERT: H 150 MET cc_start: 0.8155 (tmm) cc_final: 0.7608 (tmm) REVERT: H 168 GLU cc_start: 0.9021 (mp0) cc_final: 0.8625 (pm20) REVERT: H 216 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8593 (t0) REVERT: H 330 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9155 (pp) REVERT: H 394 THR cc_start: 0.9209 (p) cc_final: 0.8921 (p) REVERT: H 395 GLU cc_start: 0.8459 (mp0) cc_final: 0.8171 (mp0) REVERT: H 505 SER cc_start: 0.8978 (t) cc_final: 0.8718 (t) REVERT: H 512 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7908 (ttp80) REVERT: P 1 MET cc_start: 0.5851 (OUTLIER) cc_final: 0.2960 (pp-130) outliers start: 163 outliers final: 107 residues processed: 1022 average time/residue: 0.4305 time to fit residues: 714.1889 Evaluate side-chains 1010 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 873 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 309 GLN Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 512 ARG Chi-restraints excluded: chain P residue 1 MET 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: 2.9990 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 0.0770 chunk 45 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 311 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103875 restraints weight = 51563.422| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.41 r_work: 0.3079 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32352 Z= 0.180 Angle : 0.686 10.079 43936 Z= 0.325 Chirality : 0.046 0.177 5000 Planarity : 0.004 0.051 5456 Dihedral : 14.350 171.871 5358 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.68 % Allowed : 29.13 % Favored : 66.20 % 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: -1.19 (0.13), residues: 3968 helix: -0.11 (0.14), residues: 1296 sheet: -1.56 (0.23), residues: 488 loop : -0.96 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 466 PHE 0.025 0.001 PHE F 401 TYR 0.012 0.001 TYR F 459 ARG 0.010 0.001 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11106.68 seconds wall clock time: 201 minutes 1.60 seconds (12061.60 seconds total)