Starting phenix.real_space_refine on Wed Feb 21 20:14:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua4_20705/02_2024/6ua4_20705_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua4_20705/02_2024/6ua4_20705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua4_20705/02_2024/6ua4_20705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua4_20705/02_2024/6ua4_20705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua4_20705/02_2024/6ua4_20705_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua4_20705/02_2024/6ua4_20705_updated.pdb" } resolution = 3.65 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= 0.074 sd= 2.929 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 90 5.49 5 S 176 5.16 5 C 19716 2.51 5 N 5430 2.21 5 O 6314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B PHE 401": "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 ARG 407": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D 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 PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E 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 PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 407": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ARG 407": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31726 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 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: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 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: 17.02, per 1000 atoms: 0.54 Number of scatterers: 31726 At special positions: 0 Unit cell: (151.2, 150.15, 122.85, 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 90 15.00 O 6314 8.00 N 5430 7.00 C 19716 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=0, symmetry=0 Time building additional restraints: 12.29 Conformation dependent library (CDL) restraints added in 6.1 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: 150 helices and 49 sheets defined 31.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.44 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 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 128 through 137 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 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.731A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 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: 4.227A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 499 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 removed outlier: 3.542A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 128 through 137 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 194 through 204 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.520A pdb=" N LYS B 257 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR B 258 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.903A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 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 354 removed outlier: 3.916A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 removed outlier: 3.669A pdb=" N LEU B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) 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 495 through 501 removed outlier: 3.632A pdb=" N VAL B 499 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU B 500 " --> pdb=" O SER B 496 " (cutoff:3.500A) 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 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 128 through 137 removed outlier: 3.780A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.520A pdb=" N LYS C 228 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 266 removed outlier: 4.535A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.516A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) 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: 3.756A pdb=" N TYR C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 377 removed outlier: 3.579A pdb=" N ALA C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 501 removed outlier: 3.886A pdb=" N GLU C 500 " --> pdb=" O SER C 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 24 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 85 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 135 removed outlier: 3.555A pdb=" N PHE D 131 " --> pdb=" O ARG D 128 " (cutoff:3.500A) 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: 3.710A pdb=" N LYS D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 262 " --> pdb=" O ARG D 259 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN D 265 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 Processing helix chain 'D' and resid 308 through 314 removed outlier: 4.103A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.709A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 495 through 501 removed outlier: 3.866A pdb=" N VAL D 499 " --> pdb=" O SER D 495 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU D 500 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 24 removed outlier: 3.698A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 20 through 24' 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: 3.689A pdb=" N ALA E 135 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS E 137 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.581A pdb=" N LYS E 257 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 262 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 3.897A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.886A 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: 4.466A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 417 through 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 499 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 removed outlier: 3.777A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 removed outlier: 3.509A pdb=" N VAL F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 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 194 through 204 Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.675A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 3.905A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 removed outlier: 4.394A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) 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 355 removed outlier: 3.966A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (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 495 through 501 removed outlier: 3.621A pdb=" N VAL F 499 " --> pdb=" O SER F 495 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU F 500 " --> pdb=" O SER F 496 " (cutoff:3.500A) 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 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 128 through 137 removed outlier: 4.040A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 225 through 229 removed outlier: 3.572A pdb=" N LYS G 228 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.569A pdb=" N LYS G 257 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 290 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: 3.988A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 377 Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 501 removed outlier: 3.750A pdb=" N VAL G 499 " --> pdb=" O SER G 495 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU G 500 " --> pdb=" O SER G 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 24 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 83 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.538A pdb=" N PHE H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) 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: 3.527A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU H 262 " --> pdb=" O ARG H 259 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN H 265 " --> pdb=" O LEU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 307 through 314 removed outlier: 4.340A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) 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: 3.761A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) removed outlier: 4.304A 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 417 through 419 No H-bonds generated for 'chain 'H' and resid 417 through 419' 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 484 Processing helix chain 'H' and resid 495 through 501 Processing helix chain 'M' and resid 2 through 5 No H-bonds generated for 'chain 'M' and resid 2 through 5' Processing helix chain 'N' and resid 2 through 5 No H-bonds generated for 'chain 'N' and resid 2 through 5' Processing helix chain 'O' and resid 2 through 5 No H-bonds generated for 'chain 'O' and resid 2 through 5' Processing helix chain 'I' and resid 2 through 5 No H-bonds generated for 'chain 'I' and resid 2 through 5' Processing helix chain 'J' and resid 2 through 5 No H-bonds generated for 'chain 'J' and resid 2 through 5' Processing helix chain 'K' and resid 2 through 5 No H-bonds generated for 'chain 'K' and resid 2 through 5' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.581A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.809A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.768A 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 143 through 145 Processing sheet with id= F, first strand: chain 'A' and resid 209 through 212 removed outlier: 3.909A 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 37 Processing sheet with id= H, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.896A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 363 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.667A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL B 272 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 6.891A 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 Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 65 through 67 removed outlier: 5.992A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 383 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 120 through 122 Processing sheet with id= P, first strand: chain 'C' and resid 248 through 250 removed outlier: 6.711A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 401 through 403 removed outlier: 3.568A pdb=" N LEU C 408 " --> pdb=" O PHE C 401 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 409 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= S, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.262A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 120 through 122 Processing sheet with id= U, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.877A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL D 272 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.144A 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 400 through 403 removed outlier: 3.594A pdb=" N SER D 403 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 209 through 212 Processing sheet with id= X, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Y, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.310A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.916A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 320 through 323 removed outlier: 7.477A pdb=" N VAL E 323 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE E 362 " --> pdb=" O VAL E 323 " (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: 3.760A 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 37 Processing sheet with id= AF, first strand: chain 'F' and resid 65 through 67 removed outlier: 5.885A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 89 through 91 removed outlier: 6.504A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 320 through 323 removed outlier: 7.525A pdb=" N VAL F 323 " --> pdb=" O PRO F 360 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE F 362 " --> pdb=" O VAL F 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 400 through 403 Processing sheet with id= AJ, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AK, first strand: chain 'F' and resid 208 through 212 Processing sheet with id= AL, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AM, first strand: chain 'G' and resid 65 through 67 removed outlier: 5.890A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR G 383 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 248 through 250 removed outlier: 6.710A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 401 through 403 removed outlier: 3.533A pdb=" N LEU G 408 " --> pdb=" O PHE G 401 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AQ, first strand: chain 'G' and resid 208 through 212 removed outlier: 3.632A pdb=" N ILE G 222 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE G 211 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AS, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.034A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR H 383 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 120 through 122 Processing sheet with id= AU, first strand: chain 'H' and resid 187 through 189 Processing sheet with id= AV, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.976A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'H' and resid 400 through 403 removed outlier: 3.666A pdb=" N SER H 403 " --> pdb=" O ILE H 406 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2037 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: 10.49 Time building geometry restraints manager: 13.29 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: 5321 1.30 - 1.43: 7728 1.43 - 1.56: 18728 1.56 - 1.68: 207 1.68 - 1.81: 298 Bond restraints: 32282 Sorted by residual: bond pdb=" C2' ATP F 603 " pdb=" C3' ATP F 603 " ideal model delta sigma weight residual 1.531 1.240 0.291 1.20e-02 6.94e+03 5.89e+02 bond pdb=" C2' ATP E 603 " pdb=" C3' ATP E 603 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.81e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.243 0.288 1.20e-02 6.94e+03 5.75e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.245 0.286 1.20e-02 6.94e+03 5.67e+02 bond pdb=" C2' ATP D 603 " pdb=" C3' ATP D 603 " ideal model delta sigma weight residual 1.531 1.248 0.283 1.20e-02 6.94e+03 5.56e+02 ... (remaining 32277 not shown) Histogram of bond angle deviations from ideal: 93.85 - 103.57: 438 103.57 - 113.28: 18396 113.28 - 123.00: 22884 123.00 - 132.71: 2023 132.71 - 142.42: 83 Bond angle restraints: 43824 Sorted by residual: angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 118.87 21.00 1.00e+00 1.00e+00 4.41e+02 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 119.33 20.54 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 119.48 20.39 1.00e+00 1.00e+00 4.16e+02 angle pdb=" PB ATP F 603 " pdb=" O3B ATP F 603 " pdb=" PG ATP F 603 " ideal model delta sigma weight residual 139.87 120.45 19.42 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 ... (remaining 43819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 19203 35.84 - 71.68: 533 71.68 - 107.52: 44 107.52 - 143.36: 21 143.36 - 179.20: 19 Dihedral angle restraints: 19820 sinusoidal: 8412 harmonic: 11408 Sorted by residual: dihedral pdb=" CA SER L 11 " pdb=" C SER L 11 " pdb=" N TYR L 12 " pdb=" CA TYR L 12 " ideal model delta harmonic sigma weight residual 180.00 137.57 42.43 0 5.00e+00 4.00e-02 7.20e+01 dihedral pdb=" CA SER J 11 " pdb=" C SER J 11 " pdb=" N TYR J 12 " pdb=" CA TYR J 12 " ideal model delta harmonic sigma weight residual 180.00 141.17 38.83 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA SER N 11 " pdb=" C SER N 11 " pdb=" N TYR N 12 " pdb=" CA TYR N 12 " ideal model delta harmonic sigma weight residual 180.00 142.52 37.48 0 5.00e+00 4.00e-02 5.62e+01 ... (remaining 19817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3637 0.072 - 0.144: 1151 0.144 - 0.217: 142 0.217 - 0.289: 44 0.289 - 0.361: 18 Chirality restraints: 4992 Sorted by residual: chirality pdb=" C3D NAD C 604 " pdb=" C2D NAD C 604 " pdb=" C4D NAD C 604 " pdb=" O3D NAD C 604 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C3D NAD E 605 " pdb=" C2D NAD E 605 " pdb=" C4D NAD E 605 " pdb=" O3D NAD E 605 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C3B NAD G 604 " pdb=" C2B NAD G 604 " pdb=" C4B NAD G 604 " pdb=" O3B NAD G 604 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 4989 not shown) Planarity restraints: 5454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 115 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ILE F 115 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE F 115 " -0.020 2.00e-02 2.50e+03 pdb=" N THR F 116 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 465 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C GLN G 465 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN G 465 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS G 466 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 109 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C LYS B 109 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 109 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR B 110 " 0.015 2.00e-02 2.50e+03 ... (remaining 5451 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6258 2.76 - 3.30: 30059 3.30 - 3.83: 55845 3.83 - 4.37: 64637 4.37 - 4.90: 107389 Nonbonded interactions: 264188 Sorted by model distance: nonbonded pdb=" OG SER E 329 " pdb=" O HIS H 504 " model vdw 2.226 2.440 nonbonded pdb=" OG SER A 329 " pdb=" O HIS D 504 " model vdw 2.232 2.440 nonbonded pdb=" OE1 GLU G 500 " pdb=" OG1 THR H 31 " model vdw 2.253 2.440 nonbonded pdb=" OG SER E 505 " pdb=" OE1 GLN F 368 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR A 31 " pdb=" OE1 GLU D 500 " model vdw 2.263 2.440 ... (remaining 264183 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' and resid 11 through 514) selection = (chain 'B' and resid 11 through 514) selection = (chain 'C' and resid 11 through 514) selection = (chain 'D' and resid 11 through 514) selection = (chain 'E' and resid 11 through 514) selection = (chain 'F' and resid 11 through 514) selection = (chain 'G' and resid 11 through 514) selection = (chain 'H' and resid 11 through 514) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 8.280 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 84.160 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.280 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.017 0.294 32282 Z= 1.072 Angle : 1.573 21.003 43824 Z= 0.935 Chirality : 0.071 0.361 4992 Planarity : 0.007 0.064 5454 Dihedral : 17.506 179.203 12540 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.79 % Favored : 92.19 % Rotamer: Outliers : 2.60 % Allowed : 9.66 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.26 (0.11), residues: 3968 helix: -3.58 (0.08), residues: 1292 sheet: -2.28 (0.20), residues: 608 loop : -2.45 (0.12), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS H 92 PHE 0.028 0.003 PHE H 401 TYR 0.036 0.003 TYR B 110 ARG 0.020 0.002 ARG F 355 *********************** 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 1451 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1366 time to evaluate : 3.571 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: A 16 ASP cc_start: 0.8552 (t0) cc_final: 0.8297 (t0) REVERT: A 56 THR cc_start: 0.9338 (m) cc_final: 0.8851 (p) REVERT: A 93 HIS cc_start: 0.9338 (p-80) cc_final: 0.9014 (p90) REVERT: A 103 GLU cc_start: 0.8852 (mp0) cc_final: 0.8342 (mp0) REVERT: A 134 LYS cc_start: 0.9419 (tmmm) cc_final: 0.9147 (tptm) REVERT: A 176 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8765 (tm-30) REVERT: A 199 GLU cc_start: 0.9090 (pp20) cc_final: 0.8837 (pp20) REVERT: A 231 ARG cc_start: 0.8361 (ptt90) cc_final: 0.8051 (ptp90) REVERT: A 235 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8456 (pp) REVERT: A 245 LEU cc_start: 0.8244 (mp) cc_final: 0.7939 (mp) REVERT: A 274 ASP cc_start: 0.8950 (t70) cc_final: 0.8726 (t70) REVERT: A 277 GLN cc_start: 0.8883 (tm130) cc_final: 0.8669 (tm-30) REVERT: A 281 ILE cc_start: 0.9424 (tp) cc_final: 0.9140 (tp) REVERT: A 298 GLN cc_start: 0.7637 (mt0) cc_final: 0.7127 (mt0) REVERT: A 311 LYS cc_start: 0.9158 (tmmt) cc_final: 0.8946 (tttp) REVERT: A 315 ASP cc_start: 0.8497 (t0) cc_final: 0.8219 (t0) REVERT: A 343 GLN cc_start: 0.8378 (tm130) cc_final: 0.8045 (tm130) REVERT: A 400 TYR cc_start: 0.8793 (m-80) cc_final: 0.7834 (m-80) REVERT: A 407 ARG cc_start: 0.8546 (ttp80) cc_final: 0.7749 (ttp-170) REVERT: A 414 MET cc_start: 0.8035 (mtm) cc_final: 0.7678 (mtm) REVERT: A 449 ASP cc_start: 0.7552 (m-30) cc_final: 0.7287 (m-30) REVERT: A 512 ARG cc_start: 0.7779 (tmt90) cc_final: 0.6581 (tmt90) REVERT: B 51 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9017 (pp) REVERT: B 52 THR cc_start: 0.9501 (m) cc_final: 0.9136 (t) REVERT: B 82 MET cc_start: 0.9003 (mtp) cc_final: 0.8787 (mtp) REVERT: B 94 ASN cc_start: 0.9166 (t160) cc_final: 0.8891 (t0) REVERT: B 100 GLN cc_start: 0.9243 (tt0) cc_final: 0.8938 (tt0) REVERT: B 129 ASP cc_start: 0.8997 (m-30) cc_final: 0.8696 (m-30) REVERT: B 132 GLU cc_start: 0.8904 (pp20) cc_final: 0.8179 (tp30) REVERT: B 134 LYS cc_start: 0.9328 (tmtp) cc_final: 0.9124 (tttm) REVERT: B 179 MET cc_start: 0.7890 (tmm) cc_final: 0.7514 (tmm) REVERT: B 196 GLU cc_start: 0.8494 (pm20) cc_final: 0.7732 (pm20) REVERT: B 199 GLU cc_start: 0.8369 (pp20) cc_final: 0.8028 (pp20) REVERT: B 200 ILE cc_start: 0.9507 (mt) cc_final: 0.9241 (mm) REVERT: B 206 LYS cc_start: 0.8907 (tptm) cc_final: 0.8678 (tppp) REVERT: B 215 ASP cc_start: 0.8731 (p0) cc_final: 0.7966 (p0) REVERT: B 216 ASP cc_start: 0.8987 (t70) cc_final: 0.8569 (t0) REVERT: B 228 LYS cc_start: 0.9358 (mtpt) cc_final: 0.9038 (mtpp) REVERT: B 242 LYS cc_start: 0.8186 (tppp) cc_final: 0.7889 (tppp) REVERT: B 253 HIS cc_start: 0.8819 (m90) cc_final: 0.8377 (m-70) REVERT: B 261 ASP cc_start: 0.8920 (p0) cc_final: 0.8700 (p0) REVERT: B 269 ASP cc_start: 0.7976 (m-30) cc_final: 0.7706 (m-30) REVERT: B 285 ASN cc_start: 0.8876 (m110) cc_final: 0.8359 (m-40) REVERT: B 296 ASN cc_start: 0.9019 (p0) cc_final: 0.8690 (p0) REVERT: B 332 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7800 (pp) REVERT: B 335 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7973 (mm-30) REVERT: B 403 SER cc_start: 0.9095 (t) cc_final: 0.8803 (t) REVERT: B 491 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 495 SER cc_start: 0.9466 (m) cc_final: 0.9090 (p) REVERT: C 78 MET cc_start: 0.9426 (tpp) cc_final: 0.8608 (tpp) REVERT: C 82 MET cc_start: 0.8804 (mtp) cc_final: 0.8564 (mtp) REVERT: C 108 LYS cc_start: 0.9113 (tppp) cc_final: 0.8459 (mmmt) REVERT: C 111 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8138 (mm-30) REVERT: C 173 CYS cc_start: 0.6315 (t) cc_final: 0.5469 (m) REVERT: C 179 MET cc_start: 0.5635 (pp-130) cc_final: 0.4711 (pp-130) REVERT: C 235 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8622 (pp) REVERT: C 409 LYS cc_start: 0.8499 (ptmt) cc_final: 0.8267 (ptpt) REVERT: C 452 SER cc_start: 0.9154 (p) cc_final: 0.8927 (m) REVERT: C 465 GLN cc_start: 0.9010 (tt0) cc_final: 0.8674 (tp40) REVERT: C 483 MET cc_start: 0.9522 (tmm) cc_final: 0.9126 (tmm) REVERT: C 489 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8564 (mtpp) REVERT: D 21 GLN cc_start: 0.8613 (pt0) cc_final: 0.8381 (pt0) REVERT: D 103 GLU cc_start: 0.8663 (mp0) cc_final: 0.8174 (mp0) REVERT: D 112 GLN cc_start: 0.8100 (mp10) cc_final: 0.7369 (mp10) REVERT: D 131 PHE cc_start: 0.8336 (m-10) cc_final: 0.7946 (m-80) REVERT: D 231 ARG cc_start: 0.7939 (pmt-80) cc_final: 0.7469 (pmt-80) REVERT: D 337 LEU cc_start: 0.9380 (mp) cc_final: 0.9168 (mp) REVERT: D 352 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8082 (tm-30) REVERT: D 484 TYR cc_start: 0.9337 (m-80) cc_final: 0.9103 (m-10) REVERT: D 487 GLU cc_start: 0.8740 (tt0) cc_final: 0.8532 (tt0) REVERT: D 512 ARG cc_start: 0.8374 (mtp-110) cc_final: 0.8072 (ttt-90) REVERT: E 132 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8723 (mt-10) REVERT: E 134 LYS cc_start: 0.9369 (tmmm) cc_final: 0.9114 (tptm) REVERT: E 168 GLU cc_start: 0.9024 (mp0) cc_final: 0.8739 (pm20) REVERT: E 178 ILE cc_start: 0.9199 (mp) cc_final: 0.8929 (mp) REVERT: E 206 LYS cc_start: 0.8634 (tppp) cc_final: 0.8302 (tppp) REVERT: E 231 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8570 (ttp-110) REVERT: E 235 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8500 (pp) REVERT: E 274 ASP cc_start: 0.9028 (t70) cc_final: 0.8788 (t0) REVERT: E 315 ASP cc_start: 0.8501 (t0) cc_final: 0.8211 (t0) REVERT: E 335 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8004 (tm-30) REVERT: E 352 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8498 (tm-30) REVERT: E 393 THR cc_start: 0.9086 (p) cc_final: 0.8883 (p) REVERT: E 395 GLU cc_start: 0.8794 (mp0) cc_final: 0.8526 (mp0) REVERT: E 403 SER cc_start: 0.8449 (t) cc_final: 0.7816 (p) REVERT: E 404 ASP cc_start: 0.8394 (t0) cc_final: 0.8125 (t0) REVERT: E 406 ILE cc_start: 0.8611 (mp) cc_final: 0.8290 (mp) REVERT: F 34 ASP cc_start: 0.8726 (t70) cc_final: 0.8482 (t70) REVERT: F 51 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8999 (pp) REVERT: F 52 THR cc_start: 0.9485 (m) cc_final: 0.9123 (t) REVERT: F 91 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8565 (pp) REVERT: F 94 ASN cc_start: 0.9209 (t160) cc_final: 0.8927 (t0) REVERT: F 95 CYS cc_start: 0.8787 (p) cc_final: 0.8583 (p) REVERT: F 100 GLN cc_start: 0.9093 (tt0) cc_final: 0.8737 (tt0) REVERT: F 111 GLU cc_start: 0.7075 (pm20) cc_final: 0.6815 (pm20) REVERT: F 125 ASP cc_start: 0.8716 (p0) cc_final: 0.8446 (p0) REVERT: F 129 ASP cc_start: 0.8553 (m-30) cc_final: 0.8217 (m-30) REVERT: F 146 ASP cc_start: 0.9030 (p0) cc_final: 0.8763 (p0) REVERT: F 164 ASP cc_start: 0.7422 (t70) cc_final: 0.6955 (t70) REVERT: F 198 ASN cc_start: 0.9197 (m110) cc_final: 0.8907 (m-40) REVERT: F 200 ILE cc_start: 0.9563 (mt) cc_final: 0.9230 (mt) REVERT: F 206 LYS cc_start: 0.9003 (tppp) cc_final: 0.8733 (tppp) REVERT: F 215 ASP cc_start: 0.9283 (m-30) cc_final: 0.8731 (t0) REVERT: F 216 ASP cc_start: 0.8833 (t70) cc_final: 0.8480 (t0) REVERT: F 217 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8056 (mm-30) REVERT: F 224 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8267 (ttp80) REVERT: F 228 LYS cc_start: 0.9331 (mtpt) cc_final: 0.8546 (mtpp) REVERT: F 232 ASP cc_start: 0.8268 (m-30) cc_final: 0.7329 (m-30) REVERT: F 241 LYS cc_start: 0.9189 (mtmt) cc_final: 0.8885 (ptpp) REVERT: F 254 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8746 (tm-30) REVERT: F 277 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8708 (tm-30) REVERT: F 309 GLN cc_start: 0.8917 (tt0) cc_final: 0.8570 (tt0) REVERT: F 332 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8275 (pp) REVERT: F 335 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8027 (mm-30) REVERT: F 352 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8322 (tm-30) REVERT: F 394 THR cc_start: 0.9046 (p) cc_final: 0.8660 (p) REVERT: F 465 GLN cc_start: 0.9018 (mt0) cc_final: 0.8698 (mt0) REVERT: F 483 MET cc_start: 0.9285 (tmm) cc_final: 0.8835 (tmm) REVERT: G 78 MET cc_start: 0.9133 (tpp) cc_final: 0.8577 (tpp) REVERT: G 108 LYS cc_start: 0.8959 (tppp) cc_final: 0.8228 (mmmt) REVERT: G 124 LYS cc_start: 0.9007 (pptt) cc_final: 0.8806 (mmtm) REVERT: G 168 GLU cc_start: 0.8514 (pp20) cc_final: 0.8256 (mp0) REVERT: G 179 MET cc_start: 0.5410 (pp-130) cc_final: 0.5125 (pp-130) REVERT: G 204 SER cc_start: 0.8231 (t) cc_final: 0.7808 (p) REVERT: G 235 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8541 (pp) REVERT: G 243 GLN cc_start: 0.8432 (mp10) cc_final: 0.8059 (mt0) REVERT: G 253 HIS cc_start: 0.8761 (m90) cc_final: 0.8483 (m-70) REVERT: G 352 GLU cc_start: 0.8851 (tp30) cc_final: 0.8588 (tp30) REVERT: G 399 GLU cc_start: 0.8588 (pm20) cc_final: 0.8272 (pm20) REVERT: G 448 GLN cc_start: 0.8624 (pt0) cc_final: 0.8381 (pt0) REVERT: G 465 GLN cc_start: 0.9026 (tt0) cc_final: 0.8333 (mm-40) REVERT: G 483 MET cc_start: 0.9469 (tmm) cc_final: 0.9139 (tmm) REVERT: G 489 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8578 (mtpp) REVERT: G 507 HIS cc_start: 0.8700 (t-90) cc_final: 0.8422 (t-90) REVERT: H 67 SER cc_start: 0.8893 (p) cc_final: 0.8666 (p) REVERT: H 109 LYS cc_start: 0.8939 (mptt) cc_final: 0.8731 (mptt) REVERT: H 115 ILE cc_start: 0.8731 (mp) cc_final: 0.8521 (mp) REVERT: H 165 PHE cc_start: 0.8438 (p90) cc_final: 0.8211 (p90) REVERT: H 176 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8715 (mp0) REVERT: H 253 HIS cc_start: 0.8593 (m90) cc_final: 0.8346 (m-70) REVERT: H 274 ASP cc_start: 0.8944 (t0) cc_final: 0.8646 (t0) REVERT: H 352 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8529 (tm-30) REVERT: H 369 ASN cc_start: 0.8844 (p0) cc_final: 0.8551 (p0) REVERT: H 496 SER cc_start: 0.9206 (p) cc_final: 0.8943 (t) REVERT: N 12 TYR cc_start: 0.8472 (t80) cc_final: 0.8232 (t80) REVERT: J 12 TYR cc_start: 0.8561 (t80) cc_final: 0.8217 (t80) outliers start: 85 outliers final: 16 residues processed: 1399 average time/residue: 0.4244 time to fit residues: 947.6281 Evaluate side-chains 993 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 968 time to evaluate : 5.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain P residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.9980 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 307 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 355 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 171 HIS ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 469 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 507 HIS B 94 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 230 ASN C 283 GLN C 309 GLN C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN D 25 ASN D 94 ASN D 265 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS D 465 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN E 343 GLN E 469 GLN E 478 GLN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN F 202 GLN F 230 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 283 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN G 498 GLN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS H 465 GLN H 498 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 32282 Z= 0.356 Angle : 0.773 10.716 43824 Z= 0.390 Chirality : 0.049 0.205 4992 Planarity : 0.005 0.051 5454 Dihedral : 18.266 179.852 5378 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 6.08 % Allowed : 18.46 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.12), residues: 3968 helix: -2.11 (0.12), residues: 1278 sheet: -2.11 (0.19), residues: 596 loop : -2.00 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 504 PHE 0.021 0.001 PHE C 99 TYR 0.033 0.002 TYR F 110 ARG 0.007 0.001 ARG F 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1049 time to evaluate : 3.495 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: A 56 THR cc_start: 0.9311 (m) cc_final: 0.9097 (m) REVERT: A 93 HIS cc_start: 0.9350 (p-80) cc_final: 0.8933 (p90) REVERT: A 95 CYS cc_start: 0.8396 (p) cc_final: 0.8083 (p) REVERT: A 103 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: A 132 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8876 (mm-30) REVERT: A 134 LYS cc_start: 0.9388 (tmmm) cc_final: 0.9133 (tptm) REVERT: A 165 PHE cc_start: 0.8316 (p90) cc_final: 0.7637 (p90) REVERT: A 176 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 206 LYS cc_start: 0.8240 (tppp) cc_final: 0.7886 (tppp) REVERT: A 231 ARG cc_start: 0.8269 (ptt90) cc_final: 0.7957 (ptp90) REVERT: A 235 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8040 (pp) REVERT: A 277 GLN cc_start: 0.8736 (tm130) cc_final: 0.8269 (tm-30) REVERT: A 298 GLN cc_start: 0.7687 (mt0) cc_final: 0.7252 (mt0) REVERT: A 315 ASP cc_start: 0.8595 (t0) cc_final: 0.8347 (t0) REVERT: A 343 GLN cc_start: 0.8506 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 395 GLU cc_start: 0.8661 (mp0) cc_final: 0.8316 (mp0) REVERT: A 498 GLN cc_start: 0.9058 (pt0) cc_final: 0.8805 (pt0) REVERT: A 510 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 37 ILE cc_start: 0.8755 (mt) cc_final: 0.8537 (mt) REVERT: B 94 ASN cc_start: 0.9258 (t0) cc_final: 0.8844 (t0) REVERT: B 100 GLN cc_start: 0.9266 (tt0) cc_final: 0.9040 (tt0) REVERT: B 110 TYR cc_start: 0.8252 (t80) cc_final: 0.8030 (t80) REVERT: B 129 ASP cc_start: 0.8994 (m-30) cc_final: 0.8374 (m-30) REVERT: B 132 GLU cc_start: 0.8970 (pp20) cc_final: 0.8671 (pp20) REVERT: B 134 LYS cc_start: 0.9242 (tmtp) cc_final: 0.9020 (tttm) REVERT: B 179 MET cc_start: 0.7855 (tmm) cc_final: 0.7516 (tmm) REVERT: B 199 GLU cc_start: 0.8278 (pp20) cc_final: 0.7997 (pp20) REVERT: B 203 ARG cc_start: 0.8629 (ptp-110) cc_final: 0.8421 (mtm110) REVERT: B 206 LYS cc_start: 0.8887 (tptm) cc_final: 0.8392 (tptp) REVERT: B 228 LYS cc_start: 0.9249 (mtpt) cc_final: 0.8977 (mtpp) REVERT: B 242 LYS cc_start: 0.8241 (tppp) cc_final: 0.7963 (tppt) REVERT: B 253 HIS cc_start: 0.8733 (m90) cc_final: 0.8464 (m-70) REVERT: B 269 ASP cc_start: 0.7956 (m-30) cc_final: 0.7624 (m-30) REVERT: B 285 ASN cc_start: 0.8874 (m110) cc_final: 0.8351 (m110) REVERT: B 332 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7731 (pp) REVERT: B 386 MET cc_start: 0.8614 (mtm) cc_final: 0.8404 (mtm) REVERT: B 403 SER cc_start: 0.8880 (t) cc_final: 0.8524 (t) REVERT: B 469 GLN cc_start: 0.9282 (tm130) cc_final: 0.9058 (tt0) REVERT: B 491 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 495 SER cc_start: 0.9486 (m) cc_final: 0.9152 (p) REVERT: C 16 ASP cc_start: 0.8371 (t0) cc_final: 0.8031 (t0) REVERT: C 78 MET cc_start: 0.9546 (tpp) cc_final: 0.8916 (tpp) REVERT: C 95 CYS cc_start: 0.8692 (p) cc_final: 0.8466 (p) REVERT: C 100 GLN cc_start: 0.9474 (tt0) cc_final: 0.9259 (tt0) REVERT: C 103 GLU cc_start: 0.8548 (mp0) cc_final: 0.8181 (mp0) REVERT: C 125 ASP cc_start: 0.8133 (p0) cc_final: 0.7266 (p0) REVERT: C 173 CYS cc_start: 0.6325 (t) cc_final: 0.5631 (m) REVERT: C 175 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7572 (mt) REVERT: C 179 MET cc_start: 0.5947 (pp-130) cc_final: 0.4545 (pp-130) REVERT: C 452 SER cc_start: 0.9164 (p) cc_final: 0.8931 (m) REVERT: C 467 SER cc_start: 0.9727 (t) cc_final: 0.9472 (p) REVERT: C 483 MET cc_start: 0.9538 (tmm) cc_final: 0.9129 (tmm) REVERT: C 489 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8558 (mtpp) REVERT: D 44 PHE cc_start: 0.9243 (p90) cc_final: 0.8998 (p90) REVERT: D 103 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: D 131 PHE cc_start: 0.8321 (m-10) cc_final: 0.7983 (m-80) REVERT: D 231 ARG cc_start: 0.7853 (pmt-80) cc_final: 0.7428 (pmt-80) REVERT: D 291 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8800 (mmmt) REVERT: D 337 LEU cc_start: 0.9362 (mp) cc_final: 0.9079 (mp) REVERT: D 352 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8047 (tm-30) REVERT: D 402 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8362 (m-10) REVERT: D 465 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8668 (mp10) REVERT: D 512 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.7996 (ttm-80) REVERT: E 75 GLU cc_start: 0.8621 (pt0) cc_final: 0.8396 (mt-10) REVERT: E 95 CYS cc_start: 0.8247 (p) cc_final: 0.8033 (p) REVERT: E 134 LYS cc_start: 0.9390 (tmmm) cc_final: 0.9112 (tptm) REVERT: E 206 LYS cc_start: 0.8776 (tppp) cc_final: 0.8461 (tppp) REVERT: E 231 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8726 (ttp-110) REVERT: E 235 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8389 (pp) REVERT: E 315 ASP cc_start: 0.8571 (t0) cc_final: 0.8324 (t0) REVERT: E 393 THR cc_start: 0.9109 (p) cc_final: 0.8808 (p) REVERT: E 395 GLU cc_start: 0.8959 (mp0) cc_final: 0.8602 (mp0) REVERT: E 403 SER cc_start: 0.8562 (t) cc_final: 0.8005 (p) REVERT: E 404 ASP cc_start: 0.8419 (t0) cc_final: 0.8065 (t0) REVERT: F 34 ASP cc_start: 0.8697 (t70) cc_final: 0.8476 (t70) REVERT: F 52 THR cc_start: 0.9417 (m) cc_final: 0.9197 (t) REVERT: F 94 ASN cc_start: 0.9274 (t0) cc_final: 0.8972 (t0) REVERT: F 100 GLN cc_start: 0.9119 (tt0) cc_final: 0.8841 (tt0) REVERT: F 128 ARG cc_start: 0.8124 (mpt180) cc_final: 0.7801 (mpp-170) REVERT: F 132 GLU cc_start: 0.8728 (pp20) cc_final: 0.8149 (tp30) REVERT: F 149 ARG cc_start: 0.7895 (mpp80) cc_final: 0.7622 (mpp80) REVERT: F 200 ILE cc_start: 0.9479 (mt) cc_final: 0.9279 (mm) REVERT: F 228 LYS cc_start: 0.9312 (mtpt) cc_final: 0.8610 (mtpp) REVERT: F 232 ASP cc_start: 0.8173 (m-30) cc_final: 0.7784 (m-30) REVERT: F 277 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8760 (tm-30) REVERT: F 332 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8003 (pp) REVERT: F 352 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8403 (tm-30) REVERT: F 465 GLN cc_start: 0.9133 (mt0) cc_final: 0.8778 (mt0) REVERT: F 483 MET cc_start: 0.9338 (tmm) cc_final: 0.8911 (tmm) REVERT: G 16 ASP cc_start: 0.8207 (t0) cc_final: 0.7918 (t0) REVERT: G 78 MET cc_start: 0.9355 (tpp) cc_final: 0.8828 (tpp) REVERT: G 95 CYS cc_start: 0.8988 (p) cc_final: 0.8709 (p) REVERT: G 108 LYS cc_start: 0.8953 (tppp) cc_final: 0.8674 (mmmt) REVERT: G 179 MET cc_start: 0.5099 (pp-130) cc_final: 0.4801 (pp-130) REVERT: G 352 GLU cc_start: 0.8879 (tp30) cc_final: 0.8641 (tp30) REVERT: G 465 GLN cc_start: 0.8911 (tt0) cc_final: 0.8485 (mm-40) REVERT: G 469 GLN cc_start: 0.9495 (tm-30) cc_final: 0.9160 (tm-30) REVERT: G 483 MET cc_start: 0.9520 (tmm) cc_final: 0.9008 (tmm) REVERT: G 489 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8545 (mtpp) REVERT: G 512 ARG cc_start: 0.8714 (mtp-110) cc_final: 0.8384 (mtm-85) REVERT: H 115 ILE cc_start: 0.8791 (mp) cc_final: 0.8558 (mp) REVERT: H 176 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8715 (mp0) REVERT: H 274 ASP cc_start: 0.8862 (t0) cc_final: 0.8607 (t0) REVERT: H 352 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8470 (tm-30) REVERT: H 416 SER cc_start: 0.8778 (p) cc_final: 0.8406 (m) REVERT: H 461 ILE cc_start: 0.9227 (mt) cc_final: 0.8869 (mt) REVERT: H 465 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8642 (mp10) REVERT: H 483 MET cc_start: 0.9310 (tmm) cc_final: 0.8686 (tmm) REVERT: H 503 VAL cc_start: 0.9373 (t) cc_final: 0.9118 (p) REVERT: L 12 TYR cc_start: 0.8548 (t80) cc_final: 0.8337 (t80) outliers start: 199 outliers final: 121 residues processed: 1144 average time/residue: 0.4060 time to fit residues: 759.2626 Evaluate side-chains 1033 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 902 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 209 LEU 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 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 167 LYS Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 465 GLN Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 3 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.5980 chunk 110 optimal weight: 8.9990 chunk 296 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 98 optimal weight: 0.0050 chunk 356 optimal weight: 9.9990 chunk 385 optimal weight: 6.9990 chunk 317 optimal weight: 0.9980 chunk 353 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS D 465 GLN D 469 GLN D 507 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 469 GLN E 478 GLN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN G 253 HIS ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32282 Z= 0.212 Angle : 0.688 9.304 43824 Z= 0.340 Chirality : 0.046 0.215 4992 Planarity : 0.004 0.049 5454 Dihedral : 17.039 177.538 5373 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 6.78 % Allowed : 21.39 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.12), residues: 3968 helix: -1.64 (0.13), residues: 1310 sheet: -1.95 (0.20), residues: 544 loop : -1.86 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 504 PHE 0.016 0.001 PHE C 99 TYR 0.033 0.002 TYR F 110 ARG 0.010 0.001 ARG C 231 *********************** 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 1223 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1001 time to evaluate : 4.853 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: A 16 ASP cc_start: 0.8575 (t0) cc_final: 0.8373 (t0) REVERT: A 93 HIS cc_start: 0.9298 (p-80) cc_final: 0.8788 (p90) REVERT: A 95 CYS cc_start: 0.8429 (p) cc_final: 0.8159 (p) REVERT: A 103 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: A 132 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8852 (mm-30) REVERT: A 134 LYS cc_start: 0.9384 (tmmm) cc_final: 0.9129 (tptm) REVERT: A 165 PHE cc_start: 0.8360 (p90) cc_final: 0.8137 (p90) REVERT: A 176 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8752 (tm-30) REVERT: A 206 LYS cc_start: 0.8145 (tppp) cc_final: 0.7751 (tppp) REVERT: A 231 ARG cc_start: 0.8310 (ptt90) cc_final: 0.7917 (ptp-110) REVERT: A 235 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8164 (pp) REVERT: A 277 GLN cc_start: 0.8678 (tm130) cc_final: 0.7555 (tm-30) REVERT: A 297 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9361 (tm) REVERT: A 315 ASP cc_start: 0.8554 (t0) cc_final: 0.8340 (t0) REVERT: A 343 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 395 GLU cc_start: 0.8751 (mp0) cc_final: 0.8398 (mp0) REVERT: A 448 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8288 (pt0) REVERT: A 478 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8604 (pp30) REVERT: A 498 GLN cc_start: 0.8861 (pt0) cc_final: 0.8587 (pt0) REVERT: A 510 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 512 ARG cc_start: 0.7672 (tmt90) cc_final: 0.6486 (tmt90) REVERT: B 16 ASP cc_start: 0.8230 (t0) cc_final: 0.7939 (t0) REVERT: B 75 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7884 (mm-30) REVERT: B 94 ASN cc_start: 0.9229 (t0) cc_final: 0.9027 (t0) REVERT: B 129 ASP cc_start: 0.9010 (m-30) cc_final: 0.8343 (m-30) REVERT: B 132 GLU cc_start: 0.8961 (pp20) cc_final: 0.8729 (pp20) REVERT: B 134 LYS cc_start: 0.9067 (tmtp) cc_final: 0.8790 (tttm) REVERT: B 179 MET cc_start: 0.7799 (tmm) cc_final: 0.7247 (ppp) REVERT: B 199 GLU cc_start: 0.8323 (pp20) cc_final: 0.8013 (pp20) REVERT: B 206 LYS cc_start: 0.8934 (tptm) cc_final: 0.8373 (tptp) REVERT: B 217 GLU cc_start: 0.8753 (mp0) cc_final: 0.8185 (mp0) REVERT: B 228 LYS cc_start: 0.9240 (mtpt) cc_final: 0.9028 (mtpp) REVERT: B 269 ASP cc_start: 0.7863 (m-30) cc_final: 0.7513 (m-30) REVERT: B 300 ILE cc_start: 0.9125 (mm) cc_final: 0.8749 (mt) REVERT: B 332 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7710 (pt) REVERT: B 335 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 364 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7459 (t0) REVERT: B 469 GLN cc_start: 0.9332 (tm130) cc_final: 0.9118 (tt0) REVERT: B 491 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 495 SER cc_start: 0.9450 (m) cc_final: 0.9089 (p) REVERT: C 78 MET cc_start: 0.9567 (tpp) cc_final: 0.8961 (tpp) REVERT: C 95 CYS cc_start: 0.8650 (p) cc_final: 0.8400 (p) REVERT: C 173 CYS cc_start: 0.6401 (t) cc_final: 0.5409 (m) REVERT: C 179 MET cc_start: 0.5929 (pp-130) cc_final: 0.4947 (pp-130) REVERT: C 337 LEU cc_start: 0.9140 (mt) cc_final: 0.8737 (mt) REVERT: C 452 SER cc_start: 0.9211 (p) cc_final: 0.8976 (m) REVERT: C 467 SER cc_start: 0.9702 (t) cc_final: 0.9400 (p) REVERT: C 483 MET cc_start: 0.9545 (tmm) cc_final: 0.9176 (tmm) REVERT: C 489 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8519 (mtpp) REVERT: D 51 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9077 (pp) REVERT: D 103 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: D 111 GLU cc_start: 0.8851 (pm20) cc_final: 0.8650 (pm20) REVERT: D 112 GLN cc_start: 0.7398 (mp10) cc_final: 0.6972 (mp10) REVERT: D 131 PHE cc_start: 0.8362 (m-10) cc_final: 0.8022 (m-80) REVERT: D 231 ARG cc_start: 0.7858 (pmt-80) cc_final: 0.7414 (pmt-80) REVERT: D 291 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8756 (mmmt) REVERT: D 352 GLU cc_start: 0.8662 (tm-30) cc_final: 0.7984 (tm-30) REVERT: D 465 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8780 (mp10) REVERT: D 480 ARG cc_start: 0.9223 (mtm-85) cc_final: 0.8824 (mtm-85) REVERT: D 483 MET cc_start: 0.9273 (tmm) cc_final: 0.8616 (tmm) REVERT: D 512 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.7815 (ttm-80) REVERT: E 132 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8933 (mm-30) REVERT: E 134 LYS cc_start: 0.9384 (tmmm) cc_final: 0.9118 (tptm) REVERT: E 206 LYS cc_start: 0.8733 (tppp) cc_final: 0.8448 (tppp) REVERT: E 231 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8803 (tmm-80) REVERT: E 235 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8387 (pp) REVERT: E 263 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9113 (mp) REVERT: E 277 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7775 (tm-30) REVERT: E 315 ASP cc_start: 0.8557 (t0) cc_final: 0.8338 (t0) REVERT: E 393 THR cc_start: 0.8951 (p) cc_final: 0.8717 (p) REVERT: E 395 GLU cc_start: 0.8840 (mp0) cc_final: 0.8454 (mp0) REVERT: E 403 SER cc_start: 0.8588 (t) cc_final: 0.8133 (p) REVERT: E 404 ASP cc_start: 0.8351 (t0) cc_final: 0.8080 (t0) REVERT: E 448 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8145 (pt0) REVERT: E 512 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7673 (ttp80) REVERT: F 34 ASP cc_start: 0.8610 (t70) cc_final: 0.8386 (t70) REVERT: F 94 ASN cc_start: 0.9228 (t0) cc_final: 0.9010 (t0) REVERT: F 132 GLU cc_start: 0.8774 (pp20) cc_final: 0.8535 (pp20) REVERT: F 176 GLU cc_start: 0.7357 (mp0) cc_final: 0.7006 (mp0) REVERT: F 206 LYS cc_start: 0.9142 (tppp) cc_final: 0.8798 (tppp) REVERT: F 228 LYS cc_start: 0.9244 (mtpt) cc_final: 0.8529 (mtpp) REVERT: F 232 ASP cc_start: 0.8274 (m-30) cc_final: 0.7858 (m-30) REVERT: F 309 GLN cc_start: 0.8818 (tt0) cc_final: 0.8007 (tt0) REVERT: F 332 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.7979 (pp) REVERT: F 465 GLN cc_start: 0.9039 (mt0) cc_final: 0.8807 (mt0) REVERT: F 483 MET cc_start: 0.9359 (tmm) cc_final: 0.9008 (tmm) REVERT: G 95 CYS cc_start: 0.8976 (p) cc_final: 0.8675 (p) REVERT: G 100 GLN cc_start: 0.9554 (tt0) cc_final: 0.9181 (tt0) REVERT: G 108 LYS cc_start: 0.8925 (tppp) cc_final: 0.8542 (tppt) REVERT: G 179 MET cc_start: 0.5198 (pp-130) cc_final: 0.4722 (pp-130) REVERT: G 343 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: G 465 GLN cc_start: 0.8859 (tt0) cc_final: 0.8333 (mm110) REVERT: G 483 MET cc_start: 0.9489 (tmm) cc_final: 0.8997 (tmm) REVERT: G 512 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8377 (ttp-110) REVERT: H 15 ASP cc_start: 0.7925 (p0) cc_final: 0.7662 (p0) REVERT: H 51 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8990 (pp) REVERT: H 115 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8626 (mp) REVERT: H 165 PHE cc_start: 0.8041 (p90) cc_final: 0.7825 (p90) REVERT: H 176 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8706 (mp0) REVERT: H 274 ASP cc_start: 0.8884 (t0) cc_final: 0.8627 (t0) REVERT: H 297 LEU cc_start: 0.9366 (tp) cc_final: 0.8873 (tt) REVERT: H 352 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8421 (tm-30) REVERT: H 416 SER cc_start: 0.8732 (p) cc_final: 0.8354 (m) REVERT: H 482 MET cc_start: 0.9110 (mtp) cc_final: 0.8782 (mtp) REVERT: M 4 TYR cc_start: 0.9320 (t80) cc_final: 0.9117 (t80) REVERT: K 1 MET cc_start: 0.6073 (tpp) cc_final: 0.5840 (tpp) outliers start: 222 outliers final: 119 residues processed: 1110 average time/residue: 0.3985 time to fit residues: 726.2136 Evaluate side-chains 1051 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 915 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 488 LEU Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 3 ASP Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 0.6980 chunk 268 optimal weight: 0.0000 chunk 185 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 357 optimal weight: 20.0000 chunk 378 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 339 optimal weight: 0.0050 chunk 102 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 277 GLN A 309 GLN ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS D 465 GLN D 498 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 GLN E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN ** H 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32282 Z= 0.173 Angle : 0.666 10.640 43824 Z= 0.325 Chirality : 0.046 0.231 4992 Planarity : 0.004 0.046 5454 Dihedral : 16.231 179.866 5369 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 7.03 % Allowed : 22.80 % Favored : 70.17 % 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: -2.46 (0.12), residues: 3968 helix: -1.31 (0.13), residues: 1312 sheet: -1.89 (0.20), residues: 556 loop : -1.73 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 92 PHE 0.020 0.001 PHE D 490 TYR 0.020 0.001 TYR F 110 ARG 0.012 0.000 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1017 time to evaluate : 3.649 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 93 HIS cc_start: 0.9143 (p-80) cc_final: 0.8702 (p90) REVERT: A 95 CYS cc_start: 0.8461 (p) cc_final: 0.8132 (p) REVERT: A 103 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: A 132 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8669 (tp30) REVERT: A 134 LYS cc_start: 0.9370 (tmmm) cc_final: 0.9149 (tptm) REVERT: A 165 PHE cc_start: 0.8266 (p90) cc_final: 0.7634 (p90) REVERT: A 176 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8779 (tm-30) REVERT: A 179 MET cc_start: 0.7405 (ttp) cc_final: 0.6999 (tmm) REVERT: A 206 LYS cc_start: 0.8160 (tppp) cc_final: 0.7777 (tppp) REVERT: A 231 ARG cc_start: 0.8323 (ptt90) cc_final: 0.7976 (ptp-110) REVERT: A 235 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7926 (pp) REVERT: A 277 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8004 (tp40) REVERT: A 298 GLN cc_start: 0.7570 (mt0) cc_final: 0.7213 (mt0) REVERT: A 312 ASN cc_start: 0.9154 (t0) cc_final: 0.8570 (t0) REVERT: A 315 ASP cc_start: 0.8506 (t0) cc_final: 0.8279 (t0) REVERT: A 331 CYS cc_start: 0.8698 (t) cc_final: 0.8265 (t) REVERT: A 343 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 395 GLU cc_start: 0.8720 (mp0) cc_final: 0.8079 (mp0) REVERT: A 448 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: A 478 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8556 (pp30) REVERT: A 498 GLN cc_start: 0.8735 (pt0) cc_final: 0.8399 (pt0) REVERT: A 512 ARG cc_start: 0.7765 (tmt90) cc_final: 0.6667 (tmt90) REVERT: B 16 ASP cc_start: 0.8233 (t0) cc_final: 0.7871 (t0) REVERT: B 132 GLU cc_start: 0.8953 (pp20) cc_final: 0.8674 (pp20) REVERT: B 179 MET cc_start: 0.7766 (tmm) cc_final: 0.7263 (ppp) REVERT: B 193 THR cc_start: 0.9311 (t) cc_final: 0.9076 (p) REVERT: B 199 GLU cc_start: 0.8326 (pp20) cc_final: 0.7837 (pp20) REVERT: B 203 ARG cc_start: 0.8708 (ptp-110) cc_final: 0.8345 (mtm110) REVERT: B 206 LYS cc_start: 0.8941 (tptm) cc_final: 0.8330 (tptp) REVERT: B 269 ASP cc_start: 0.7818 (m-30) cc_final: 0.7524 (m-30) REVERT: B 332 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7153 (tp) REVERT: B 364 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7375 (t0) REVERT: B 412 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7635 (ptt90) REVERT: B 491 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: B 495 SER cc_start: 0.9441 (m) cc_final: 0.9074 (p) REVERT: C 78 MET cc_start: 0.9564 (tpp) cc_final: 0.9006 (tpp) REVERT: C 95 CYS cc_start: 0.8690 (p) cc_final: 0.8474 (p) REVERT: C 173 CYS cc_start: 0.6346 (t) cc_final: 0.5343 (m) REVERT: C 179 MET cc_start: 0.5973 (pp-130) cc_final: 0.4941 (pp-130) REVERT: C 337 LEU cc_start: 0.9097 (mt) cc_final: 0.8736 (mt) REVERT: C 452 SER cc_start: 0.9243 (p) cc_final: 0.9002 (m) REVERT: C 465 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8505 (mm-40) REVERT: C 467 SER cc_start: 0.9759 (t) cc_final: 0.9350 (p) REVERT: C 483 MET cc_start: 0.9533 (tmm) cc_final: 0.9155 (tmm) REVERT: C 488 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.8867 (tt) REVERT: C 500 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 512 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8388 (ttp-110) REVERT: D 51 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9041 (pp) REVERT: D 103 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: D 131 PHE cc_start: 0.8376 (m-10) cc_final: 0.8053 (m-80) REVERT: D 215 ASP cc_start: 0.8393 (t0) cc_final: 0.8181 (t0) REVERT: D 291 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8639 (mmmt) REVERT: D 332 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8605 (pp) REVERT: D 334 GLN cc_start: 0.9063 (mt0) cc_final: 0.8758 (mt0) REVERT: D 393 THR cc_start: 0.9175 (p) cc_final: 0.8970 (p) REVERT: D 402 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: D 483 MET cc_start: 0.9306 (tmm) cc_final: 0.8608 (tmm) REVERT: E 41 TYR cc_start: 0.9037 (t80) cc_final: 0.8789 (t80) REVERT: E 132 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8859 (mt-10) REVERT: E 134 LYS cc_start: 0.9383 (tmmm) cc_final: 0.9114 (tptm) REVERT: E 231 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8751 (tmm-80) REVERT: E 235 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8320 (pp) REVERT: E 263 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9019 (mp) REVERT: E 277 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7758 (tm-30) REVERT: E 285 ASN cc_start: 0.9123 (m110) cc_final: 0.8549 (m-40) REVERT: E 315 ASP cc_start: 0.8559 (t0) cc_final: 0.8337 (t0) REVERT: E 332 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8611 (pp) REVERT: E 369 ASN cc_start: 0.8868 (p0) cc_final: 0.8415 (p0) REVERT: E 403 SER cc_start: 0.8675 (t) cc_final: 0.8259 (p) REVERT: E 404 ASP cc_start: 0.8356 (t0) cc_final: 0.8074 (t0) REVERT: E 448 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: F 34 ASP cc_start: 0.8581 (t70) cc_final: 0.8365 (t70) REVERT: F 111 GLU cc_start: 0.6920 (pm20) cc_final: 0.6488 (pm20) REVERT: F 128 ARG cc_start: 0.7664 (mpt180) cc_final: 0.7085 (mpt180) REVERT: F 132 GLU cc_start: 0.8761 (pp20) cc_final: 0.8467 (pp20) REVERT: F 161 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8153 (mtt90) REVERT: F 185 LEU cc_start: 0.8620 (tp) cc_final: 0.8064 (mt) REVERT: F 202 GLN cc_start: 0.9262 (pt0) cc_final: 0.9042 (pt0) REVERT: F 228 LYS cc_start: 0.9280 (mtpt) cc_final: 0.8625 (mtpp) REVERT: F 232 ASP cc_start: 0.8427 (m-30) cc_final: 0.7886 (m-30) REVERT: F 319 ASP cc_start: 0.7666 (t0) cc_final: 0.6863 (t0) REVERT: F 332 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7877 (pp) REVERT: F 334 GLN cc_start: 0.8535 (pp30) cc_final: 0.8166 (pp30) REVERT: F 364 ASP cc_start: 0.7752 (m-30) cc_final: 0.7460 (t0) REVERT: F 465 GLN cc_start: 0.9039 (mt0) cc_final: 0.8754 (mt0) REVERT: F 483 MET cc_start: 0.9394 (tmm) cc_final: 0.8923 (tmm) REVERT: G 95 CYS cc_start: 0.8980 (p) cc_final: 0.8752 (p) REVERT: G 108 LYS cc_start: 0.8806 (tppp) cc_final: 0.8484 (tppt) REVERT: G 179 MET cc_start: 0.5018 (pp-130) cc_final: 0.4686 (pp-130) REVERT: G 258 TYR cc_start: 0.9171 (t80) cc_final: 0.8924 (t80) REVERT: G 283 GLN cc_start: 0.8949 (tt0) cc_final: 0.8628 (tt0) REVERT: G 343 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: G 465 GLN cc_start: 0.8784 (tt0) cc_final: 0.8289 (mm110) REVERT: G 483 MET cc_start: 0.9481 (tmm) cc_final: 0.8939 (tmm) REVERT: G 512 ARG cc_start: 0.8679 (mtp-110) cc_final: 0.8381 (ttp-110) REVERT: H 15 ASP cc_start: 0.7992 (p0) cc_final: 0.7719 (p0) REVERT: H 51 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9045 (pp) REVERT: H 78 MET cc_start: 0.9079 (tpp) cc_final: 0.7446 (tpp) REVERT: H 115 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8614 (mp) REVERT: H 150 MET cc_start: 0.9246 (tmm) cc_final: 0.8985 (tmm) REVERT: H 163 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7156 (mm) REVERT: H 165 PHE cc_start: 0.8057 (p90) cc_final: 0.7807 (p90) REVERT: H 176 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8703 (mp0) REVERT: H 274 ASP cc_start: 0.8783 (t0) cc_final: 0.8565 (t0) REVERT: H 352 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8370 (tm-30) REVERT: H 393 THR cc_start: 0.8921 (p) cc_final: 0.8377 (p) REVERT: H 416 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8279 (m) outliers start: 230 outliers final: 148 residues processed: 1134 average time/residue: 0.3941 time to fit residues: 734.0943 Evaluate side-chains 1073 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 901 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 311 LYS 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 384 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 3 ASP Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 282 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 323 optimal weight: 0.5980 chunk 261 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 343 GLN C 469 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 32282 Z= 0.448 Angle : 0.771 9.682 43824 Z= 0.386 Chirality : 0.050 0.240 4992 Planarity : 0.004 0.050 5454 Dihedral : 16.045 174.886 5367 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 8.71 % Allowed : 22.52 % Favored : 68.77 % 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: -2.37 (0.13), residues: 3968 helix: -1.28 (0.13), residues: 1342 sheet: -1.83 (0.22), residues: 484 loop : -1.68 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 504 PHE 0.019 0.002 PHE H 490 TYR 0.021 0.002 TYR F 110 ARG 0.009 0.001 ARG F 203 *********************** 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 1194 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 909 time to evaluate : 3.670 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: A 95 CYS cc_start: 0.8343 (p) cc_final: 0.8094 (p) REVERT: A 103 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: A 132 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8727 (tp30) REVERT: A 165 PHE cc_start: 0.8436 (p90) cc_final: 0.7787 (p90) REVERT: A 176 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8781 (tm-30) REVERT: A 179 MET cc_start: 0.7370 (ttp) cc_final: 0.7066 (tmm) REVERT: A 206 LYS cc_start: 0.8443 (tppp) cc_final: 0.8024 (tppp) REVERT: A 235 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8091 (pp) REVERT: A 331 CYS cc_start: 0.8908 (t) cc_final: 0.8518 (t) REVERT: A 343 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 395 GLU cc_start: 0.8738 (mp0) cc_final: 0.8315 (mp0) REVERT: A 448 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: A 478 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8748 (pp30) REVERT: A 506 LEU cc_start: 0.9228 (mm) cc_final: 0.9023 (mm) REVERT: A 512 ARG cc_start: 0.7790 (tmt90) cc_final: 0.6622 (tmt90) REVERT: B 129 ASP cc_start: 0.9043 (m-30) cc_final: 0.8360 (m-30) REVERT: B 132 GLU cc_start: 0.8973 (pp20) cc_final: 0.8659 (pp20) REVERT: B 136 ARG cc_start: 0.9220 (mmm-85) cc_final: 0.8962 (mmm-85) REVERT: B 185 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8601 (tm) REVERT: B 199 GLU cc_start: 0.8439 (pp20) cc_final: 0.7968 (pp20) REVERT: B 203 ARG cc_start: 0.8765 (ptp-110) cc_final: 0.8509 (mtm110) REVERT: B 206 LYS cc_start: 0.8985 (tptm) cc_final: 0.8691 (tptp) REVERT: B 269 ASP cc_start: 0.7939 (m-30) cc_final: 0.7636 (m-30) REVERT: B 286 MET cc_start: 0.9021 (tpp) cc_final: 0.8721 (tpp) REVERT: B 332 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7952 (pt) REVERT: B 352 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8449 (tm-30) REVERT: B 364 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7791 (t0) REVERT: B 469 GLN cc_start: 0.9460 (OUTLIER) cc_final: 0.9042 (tt0) REVERT: B 491 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: B 495 SER cc_start: 0.9485 (m) cc_final: 0.9167 (p) REVERT: C 173 CYS cc_start: 0.6560 (t) cc_final: 0.5421 (m) REVERT: C 179 MET cc_start: 0.5973 (pp-130) cc_final: 0.4952 (pp-130) REVERT: C 204 SER cc_start: 0.8177 (t) cc_final: 0.7763 (p) REVERT: C 337 LEU cc_start: 0.9172 (mt) cc_final: 0.8972 (mt) REVERT: C 343 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: C 368 GLN cc_start: 0.8476 (pm20) cc_final: 0.8241 (pm20) REVERT: C 452 SER cc_start: 0.9295 (p) cc_final: 0.9007 (m) REVERT: C 467 SER cc_start: 0.9728 (t) cc_final: 0.9315 (p) REVERT: C 483 MET cc_start: 0.9551 (tmm) cc_final: 0.9133 (tmm) REVERT: C 512 ARG cc_start: 0.8865 (mtp-110) cc_final: 0.8463 (ttp-110) REVERT: D 78 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8476 (ttp) REVERT: D 103 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: D 112 GLN cc_start: 0.7608 (mp10) cc_final: 0.7302 (mp-120) REVERT: D 131 PHE cc_start: 0.8394 (m-10) cc_final: 0.8057 (m-80) REVERT: D 215 ASP cc_start: 0.8399 (t0) cc_final: 0.8188 (t0) REVERT: D 231 ARG cc_start: 0.8264 (ptm160) cc_final: 0.8048 (ptm160) REVERT: D 277 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7975 (tm-30) REVERT: D 291 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8563 (mmtt) REVERT: D 332 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8708 (pp) REVERT: D 352 GLU cc_start: 0.8731 (tm-30) cc_final: 0.7955 (tm-30) REVERT: D 390 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9132 (mp) REVERT: D 483 MET cc_start: 0.9351 (tmm) cc_final: 0.8674 (tmm) REVERT: E 16 ASP cc_start: 0.8073 (t0) cc_final: 0.7869 (t0) REVERT: E 132 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8874 (tp30) REVERT: E 134 LYS cc_start: 0.9359 (tmmm) cc_final: 0.9096 (tptm) REVERT: E 203 ARG cc_start: 0.8482 (mtm-85) cc_final: 0.8247 (mtm110) REVERT: E 206 LYS cc_start: 0.8925 (tppp) cc_final: 0.8654 (tppp) REVERT: E 231 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8835 (tmm-80) REVERT: E 235 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8448 (pp) REVERT: E 263 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9082 (mp) REVERT: E 277 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8064 (tm-30) REVERT: E 315 ASP cc_start: 0.8641 (t0) cc_final: 0.8430 (t0) REVERT: E 403 SER cc_start: 0.8729 (t) cc_final: 0.8260 (p) REVERT: E 404 ASP cc_start: 0.8374 (t0) cc_final: 0.7981 (t0) REVERT: E 448 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: E 498 GLN cc_start: 0.9139 (pt0) cc_final: 0.8887 (pt0) REVERT: E 512 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7716 (ttp80) REVERT: F 34 ASP cc_start: 0.8815 (t70) cc_final: 0.8577 (t70) REVERT: F 111 GLU cc_start: 0.7211 (pm20) cc_final: 0.6892 (pm20) REVERT: F 128 ARG cc_start: 0.7781 (mpt180) cc_final: 0.7034 (mpt180) REVERT: F 132 GLU cc_start: 0.8775 (pp20) cc_final: 0.8506 (pp20) REVERT: F 176 GLU cc_start: 0.7147 (mp0) cc_final: 0.6933 (mp0) REVERT: F 203 ARG cc_start: 0.8708 (mtm110) cc_final: 0.8445 (mtm110) REVERT: F 206 LYS cc_start: 0.9218 (tppp) cc_final: 0.8870 (tppp) REVERT: F 228 LYS cc_start: 0.9244 (mtpt) cc_final: 0.8569 (mtpp) REVERT: F 232 ASP cc_start: 0.8351 (m-30) cc_final: 0.7865 (m-30) REVERT: F 319 ASP cc_start: 0.7792 (t0) cc_final: 0.7240 (t0) REVERT: F 332 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8107 (pt) REVERT: F 334 GLN cc_start: 0.8537 (pp30) cc_final: 0.8095 (pp30) REVERT: F 352 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8720 (tm-30) REVERT: F 418 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8109 (p0) REVERT: F 483 MET cc_start: 0.9349 (tmm) cc_final: 0.9112 (tmm) REVERT: G 100 GLN cc_start: 0.9575 (tt0) cc_final: 0.9171 (tt0) REVERT: G 108 LYS cc_start: 0.8974 (tppp) cc_final: 0.8623 (tppt) REVERT: G 179 MET cc_start: 0.5051 (pp-130) cc_final: 0.4798 (pp-130) REVERT: G 409 LYS cc_start: 0.8357 (ttmm) cc_final: 0.8037 (ttmm) REVERT: G 465 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8345 (mm110) REVERT: G 483 MET cc_start: 0.9531 (tmm) cc_final: 0.9134 (tmm) REVERT: G 512 ARG cc_start: 0.8817 (mtp-110) cc_final: 0.8436 (ttp-110) REVERT: H 15 ASP cc_start: 0.8056 (p0) cc_final: 0.7781 (p0) REVERT: H 16 ASP cc_start: 0.8261 (t70) cc_final: 0.7985 (t70) REVERT: H 78 MET cc_start: 0.9565 (tpp) cc_final: 0.9293 (tpp) REVERT: H 103 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: H 165 PHE cc_start: 0.8144 (p90) cc_final: 0.7851 (p90) REVERT: H 274 ASP cc_start: 0.8746 (t0) cc_final: 0.8451 (t0) REVERT: H 318 VAL cc_start: 0.9660 (t) cc_final: 0.9426 (p) REVERT: H 352 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8404 (tm-30) REVERT: H 483 MET cc_start: 0.9359 (tmm) cc_final: 0.8645 (tmm) REVERT: L 3 ASP cc_start: 0.8824 (t0) cc_final: 0.8276 (p0) outliers start: 285 outliers final: 202 residues processed: 1056 average time/residue: 0.3868 time to fit residues: 675.4569 Evaluate side-chains 1101 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 878 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 505 SER Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 513 LEU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 1.9990 chunk 341 optimal weight: 0.0670 chunk 74 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 379 optimal weight: 0.7980 chunk 314 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN B 498 GLN C 343 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 454 HIS D 465 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN E 202 GLN ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32282 Z= 0.192 Angle : 0.685 10.292 43824 Z= 0.333 Chirality : 0.046 0.234 4992 Planarity : 0.004 0.046 5454 Dihedral : 15.543 176.102 5365 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 7.00 % Allowed : 25.24 % Favored : 67.76 % 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: -2.19 (0.13), residues: 3968 helix: -1.03 (0.14), residues: 1330 sheet: -1.84 (0.21), residues: 520 loop : -1.60 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS B 504 PHE 0.022 0.001 PHE F 165 TYR 0.020 0.001 TYR F 110 ARG 0.006 0.000 ARG F 203 *********************** 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 1179 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 950 time to evaluate : 3.743 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 95 CYS cc_start: 0.8387 (p) cc_final: 0.8132 (p) REVERT: A 103 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: A 132 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8662 (tp30) REVERT: A 165 PHE cc_start: 0.8339 (p90) cc_final: 0.7715 (p90) REVERT: A 176 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8786 (tm-30) REVERT: A 179 MET cc_start: 0.7347 (ttp) cc_final: 0.7027 (tmm) REVERT: A 196 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8740 (pm20) REVERT: A 206 LYS cc_start: 0.8207 (tppp) cc_final: 0.7789 (tppp) REVERT: A 235 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7858 (pp) REVERT: A 311 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8752 (ttpp) REVERT: A 312 ASN cc_start: 0.9183 (t0) cc_final: 0.8695 (t0) REVERT: A 343 GLN cc_start: 0.8543 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 395 GLU cc_start: 0.8600 (mp0) cc_final: 0.8233 (mp0) REVERT: A 448 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: A 478 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8651 (pp30) REVERT: A 512 ARG cc_start: 0.7852 (tmt90) cc_final: 0.6721 (tmt90) REVERT: B 16 ASP cc_start: 0.8273 (t0) cc_final: 0.8068 (t70) REVERT: B 129 ASP cc_start: 0.9047 (m-30) cc_final: 0.8349 (m-30) REVERT: B 132 GLU cc_start: 0.8994 (pp20) cc_final: 0.8725 (pp20) REVERT: B 149 ARG cc_start: 0.8857 (mpp80) cc_final: 0.8275 (mpp80) REVERT: B 193 THR cc_start: 0.9350 (t) cc_final: 0.9139 (p) REVERT: B 206 LYS cc_start: 0.8971 (tptm) cc_final: 0.8640 (tptp) REVERT: B 269 ASP cc_start: 0.7857 (m-30) cc_final: 0.7553 (m-30) REVERT: B 286 MET cc_start: 0.8913 (tpp) cc_final: 0.8653 (tpp) REVERT: B 332 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7584 (pt) REVERT: B 334 GLN cc_start: 0.8383 (pp30) cc_final: 0.7976 (pp30) REVERT: B 364 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7705 (t0) REVERT: B 469 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.8759 (tt0) REVERT: B 483 MET cc_start: 0.9077 (tmm) cc_final: 0.8618 (tmm) REVERT: B 491 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: B 495 SER cc_start: 0.9393 (m) cc_final: 0.9086 (p) REVERT: C 179 MET cc_start: 0.5938 (pp-130) cc_final: 0.4899 (pp-130) REVERT: C 204 SER cc_start: 0.8184 (t) cc_final: 0.7771 (p) REVERT: C 337 LEU cc_start: 0.9078 (mt) cc_final: 0.8875 (mt) REVERT: C 452 SER cc_start: 0.9276 (p) cc_final: 0.9035 (m) REVERT: C 480 ARG cc_start: 0.9221 (mtt90) cc_final: 0.9020 (mtt90) REVERT: C 483 MET cc_start: 0.9518 (tmm) cc_final: 0.9196 (tmm) REVERT: C 500 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 512 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.8382 (mtm-85) REVERT: D 15 ASP cc_start: 0.8064 (p0) cc_final: 0.7844 (p0) REVERT: D 103 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: D 112 GLN cc_start: 0.7437 (mp10) cc_final: 0.7065 (mp-120) REVERT: D 131 PHE cc_start: 0.8378 (m-10) cc_final: 0.8169 (m-80) REVERT: D 215 ASP cc_start: 0.8445 (t0) cc_final: 0.8220 (t0) REVERT: D 291 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8564 (mmmt) REVERT: D 332 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8637 (pp) REVERT: D 334 GLN cc_start: 0.9099 (mt0) cc_final: 0.8826 (mt0) REVERT: D 352 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7932 (tm-30) REVERT: D 483 MET cc_start: 0.9358 (tmm) cc_final: 0.8657 (tmm) REVERT: E 16 ASP cc_start: 0.8203 (t0) cc_final: 0.7938 (t0) REVERT: E 82 MET cc_start: 0.8840 (ttp) cc_final: 0.7478 (tmm) REVERT: E 132 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8823 (tp30) REVERT: E 134 LYS cc_start: 0.9378 (tmmm) cc_final: 0.9132 (tptm) REVERT: E 206 LYS cc_start: 0.8873 (tppp) cc_final: 0.8569 (tppp) REVERT: E 231 ARG cc_start: 0.9077 (ttp80) cc_final: 0.8796 (tmm-80) REVERT: E 235 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8314 (pp) REVERT: E 263 LEU cc_start: 0.9239 (mp) cc_final: 0.8963 (mp) REVERT: E 277 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7899 (tm-30) REVERT: E 322 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8423 (ttm-80) REVERT: E 332 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8586 (pp) REVERT: E 403 SER cc_start: 0.8744 (t) cc_final: 0.8330 (p) REVERT: E 404 ASP cc_start: 0.8370 (t0) cc_final: 0.7974 (t0) REVERT: E 448 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: E 498 GLN cc_start: 0.8872 (pt0) cc_final: 0.8656 (pt0) REVERT: E 512 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7602 (ttp80) REVERT: F 34 ASP cc_start: 0.8604 (t70) cc_final: 0.8391 (t70) REVERT: F 111 GLU cc_start: 0.7004 (pm20) cc_final: 0.6474 (pm20) REVERT: F 128 ARG cc_start: 0.7788 (mpt180) cc_final: 0.7073 (mpt180) REVERT: F 132 GLU cc_start: 0.8801 (pp20) cc_final: 0.8509 (pp20) REVERT: F 161 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8096 (mtt90) REVERT: F 176 GLU cc_start: 0.7164 (mp0) cc_final: 0.6903 (mp0) REVERT: F 185 LEU cc_start: 0.8821 (mt) cc_final: 0.8200 (mt) REVERT: F 203 ARG cc_start: 0.8757 (mtm110) cc_final: 0.8264 (mtm110) REVERT: F 228 LYS cc_start: 0.9254 (mtpt) cc_final: 0.8604 (mtpp) REVERT: F 232 ASP cc_start: 0.8285 (m-30) cc_final: 0.7842 (m-30) REVERT: F 319 ASP cc_start: 0.7774 (t0) cc_final: 0.7234 (t0) REVERT: F 332 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7187 (tp) REVERT: F 334 GLN cc_start: 0.8534 (pp30) cc_final: 0.8063 (pp30) REVERT: F 483 MET cc_start: 0.9384 (tmm) cc_final: 0.8981 (tmm) REVERT: G 15 ASP cc_start: 0.8436 (p0) cc_final: 0.8217 (p0) REVERT: G 100 GLN cc_start: 0.9593 (tt0) cc_final: 0.9163 (tt0) REVERT: G 108 LYS cc_start: 0.8768 (tppp) cc_final: 0.8506 (tppt) REVERT: G 179 MET cc_start: 0.5000 (pp-130) cc_final: 0.4719 (pp-130) REVERT: G 258 TYR cc_start: 0.9176 (t80) cc_final: 0.8975 (t80) REVERT: G 283 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: G 465 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8325 (mm110) REVERT: G 478 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: G 483 MET cc_start: 0.9480 (tmm) cc_final: 0.9005 (tmm) REVERT: G 512 ARG cc_start: 0.8751 (mtp-110) cc_final: 0.8416 (ttp-110) REVERT: H 15 ASP cc_start: 0.8019 (p0) cc_final: 0.7766 (p0) REVERT: H 16 ASP cc_start: 0.8219 (t70) cc_final: 0.7923 (t70) REVERT: H 78 MET cc_start: 0.9529 (tpp) cc_final: 0.9002 (tpp) REVERT: H 103 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: H 110 TYR cc_start: 0.8542 (t80) cc_final: 0.8165 (t80) REVERT: H 150 MET cc_start: 0.9308 (tmm) cc_final: 0.9021 (tmm) REVERT: H 165 PHE cc_start: 0.8140 (p90) cc_final: 0.7854 (p90) REVERT: H 176 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8691 (mp0) REVERT: H 274 ASP cc_start: 0.8691 (t0) cc_final: 0.8383 (t0) REVERT: H 277 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7882 (tm-30) REVERT: H 352 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8354 (tm-30) REVERT: H 416 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8366 (m) REVERT: N 1 MET cc_start: 0.4811 (pmm) cc_final: 0.4426 (pmm) REVERT: L 3 ASP cc_start: 0.8795 (t0) cc_final: 0.8130 (p0) outliers start: 229 outliers final: 159 residues processed: 1064 average time/residue: 0.4025 time to fit residues: 702.1373 Evaluate side-chains 1073 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 891 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 314 ILE 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 343 GLN Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 322 ARG 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 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 416 SER Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain K residue 3 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 276 optimal weight: 0.6980 chunk 214 optimal weight: 0.4980 chunk 319 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 377 optimal weight: 0.0370 chunk 236 optimal weight: 0.6980 chunk 230 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 343 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS D 469 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32282 Z= 0.230 Angle : 0.696 9.774 43824 Z= 0.339 Chirality : 0.047 0.272 4992 Planarity : 0.004 0.046 5454 Dihedral : 15.227 170.529 5365 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 7.27 % Allowed : 25.34 % Favored : 67.39 % 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: -2.12 (0.13), residues: 3968 helix: -0.93 (0.14), residues: 1334 sheet: -1.80 (0.22), residues: 520 loop : -1.58 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 504 PHE 0.021 0.001 PHE F 165 TYR 0.026 0.001 TYR C 258 ARG 0.012 0.000 ARG E 203 *********************** 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 1143 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 905 time to evaluate : 3.675 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: A 95 CYS cc_start: 0.8391 (p) cc_final: 0.8130 (p) REVERT: A 100 GLN cc_start: 0.9467 (tt0) cc_final: 0.9265 (tt0) REVERT: A 103 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: A 132 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8675 (tp30) REVERT: A 165 PHE cc_start: 0.8321 (p90) cc_final: 0.7702 (p90) REVERT: A 176 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8904 (tm-30) REVERT: A 196 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8767 (pm20) REVERT: A 206 LYS cc_start: 0.8341 (tppp) cc_final: 0.7929 (tppp) REVERT: A 232 ASP cc_start: 0.8901 (t70) cc_final: 0.8557 (t70) REVERT: A 235 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7838 (pp) REVERT: A 311 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8715 (ttpp) REVERT: A 343 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 395 GLU cc_start: 0.8607 (mp0) cc_final: 0.8291 (mp0) REVERT: A 448 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8314 (pt0) REVERT: A 478 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8681 (pp30) REVERT: A 512 ARG cc_start: 0.7879 (tmt90) cc_final: 0.6664 (tmt90) REVERT: B 16 ASP cc_start: 0.8190 (t0) cc_final: 0.7875 (t70) REVERT: B 129 ASP cc_start: 0.9053 (m-30) cc_final: 0.8345 (m-30) REVERT: B 132 GLU cc_start: 0.8982 (pp20) cc_final: 0.8720 (pp20) REVERT: B 149 ARG cc_start: 0.8876 (mpp80) cc_final: 0.8290 (mpp80) REVERT: B 199 GLU cc_start: 0.8196 (pp20) cc_final: 0.7687 (pp20) REVERT: B 203 ARG cc_start: 0.8772 (ptp-110) cc_final: 0.8260 (mtm110) REVERT: B 206 LYS cc_start: 0.8964 (tptm) cc_final: 0.8630 (tptp) REVERT: B 269 ASP cc_start: 0.7900 (m-30) cc_final: 0.7601 (m-30) REVERT: B 286 MET cc_start: 0.8943 (tpp) cc_final: 0.8691 (tpp) REVERT: B 332 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.6917 (tp) REVERT: B 334 GLN cc_start: 0.8324 (pp30) cc_final: 0.7975 (pp30) REVERT: B 469 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.8933 (tt0) REVERT: B 483 MET cc_start: 0.9150 (tmm) cc_final: 0.8765 (tmm) REVERT: B 491 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: B 492 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7007 (mtpp) REVERT: B 495 SER cc_start: 0.9401 (m) cc_final: 0.9099 (p) REVERT: C 111 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7476 (mt-10) REVERT: C 179 MET cc_start: 0.6075 (pp-130) cc_final: 0.5031 (pp-130) REVERT: C 204 SER cc_start: 0.8214 (t) cc_final: 0.7790 (p) REVERT: C 452 SER cc_start: 0.9280 (p) cc_final: 0.8995 (m) REVERT: C 483 MET cc_start: 0.9529 (tmm) cc_final: 0.9167 (tmm) REVERT: C 500 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8381 (tm-30) REVERT: C 512 ARG cc_start: 0.8843 (mtp-110) cc_final: 0.8398 (mtm-85) REVERT: D 15 ASP cc_start: 0.7923 (p0) cc_final: 0.7680 (p0) REVERT: D 103 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: D 112 GLN cc_start: 0.7520 (mp10) cc_final: 0.7092 (mp-120) REVERT: D 131 PHE cc_start: 0.8497 (m-10) cc_final: 0.8192 (m-80) REVERT: D 215 ASP cc_start: 0.8448 (t0) cc_final: 0.8221 (t0) REVERT: D 291 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8530 (mmmt) REVERT: D 332 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8672 (pp) REVERT: D 334 GLN cc_start: 0.9087 (mt0) cc_final: 0.8816 (mt0) REVERT: D 352 GLU cc_start: 0.8643 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 385 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8502 (ttp) REVERT: E 16 ASP cc_start: 0.8217 (t0) cc_final: 0.7926 (t0) REVERT: E 132 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8719 (tp30) REVERT: E 134 LYS cc_start: 0.9366 (tmmm) cc_final: 0.9125 (tptm) REVERT: E 206 LYS cc_start: 0.8870 (tppp) cc_final: 0.8593 (tppt) REVERT: E 231 ARG cc_start: 0.9084 (ttp80) cc_final: 0.8797 (tmm-80) REVERT: E 235 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8417 (pp) REVERT: E 263 LEU cc_start: 0.9229 (mp) cc_final: 0.8942 (mp) REVERT: E 277 GLN cc_start: 0.8463 (tm-30) cc_final: 0.7923 (tm-30) REVERT: E 322 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8362 (ttm-80) REVERT: E 332 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8567 (pp) REVERT: E 403 SER cc_start: 0.8742 (t) cc_final: 0.8343 (p) REVERT: E 404 ASP cc_start: 0.8368 (t0) cc_final: 0.7973 (t0) REVERT: E 448 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: E 498 GLN cc_start: 0.8902 (pt0) cc_final: 0.8662 (pt0) REVERT: E 512 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7571 (ttp80) REVERT: F 34 ASP cc_start: 0.8690 (t70) cc_final: 0.8447 (t70) REVERT: F 111 GLU cc_start: 0.6979 (pm20) cc_final: 0.6586 (pm20) REVERT: F 132 GLU cc_start: 0.8782 (pp20) cc_final: 0.8486 (pp20) REVERT: F 185 LEU cc_start: 0.8805 (mt) cc_final: 0.8123 (mt) REVERT: F 203 ARG cc_start: 0.8841 (mtm110) cc_final: 0.8495 (ptp-110) REVERT: F 206 LYS cc_start: 0.9233 (tppt) cc_final: 0.8942 (tppp) REVERT: F 228 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8639 (mtpp) REVERT: F 232 ASP cc_start: 0.8286 (m-30) cc_final: 0.7864 (m-30) REVERT: F 312 ASN cc_start: 0.9171 (t0) cc_final: 0.8596 (t0) REVERT: F 319 ASP cc_start: 0.7718 (t0) cc_final: 0.7201 (t0) REVERT: F 332 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7127 (tp) REVERT: F 334 GLN cc_start: 0.8423 (pp30) cc_final: 0.7976 (pp30) REVERT: F 483 MET cc_start: 0.9376 (tmm) cc_final: 0.9127 (tmm) REVERT: G 100 GLN cc_start: 0.9561 (tt0) cc_final: 0.9088 (tt0) REVERT: G 103 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8680 (mp0) REVERT: G 108 LYS cc_start: 0.8764 (tppp) cc_final: 0.8499 (tppt) REVERT: G 179 MET cc_start: 0.5016 (pp-130) cc_final: 0.4730 (pp-130) REVERT: G 258 TYR cc_start: 0.9146 (t80) cc_final: 0.8903 (t80) REVERT: G 343 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: G 465 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8508 (mm-40) REVERT: G 478 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: G 483 MET cc_start: 0.9493 (tmm) cc_final: 0.9027 (tmm) REVERT: G 512 ARG cc_start: 0.8761 (mtp-110) cc_final: 0.8421 (ttp-110) REVERT: H 15 ASP cc_start: 0.8049 (p0) cc_final: 0.7747 (p0) REVERT: H 16 ASP cc_start: 0.8290 (t70) cc_final: 0.7961 (t70) REVERT: H 75 GLU cc_start: 0.7912 (tp30) cc_final: 0.7509 (tp30) REVERT: H 103 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: H 165 PHE cc_start: 0.8126 (p90) cc_final: 0.7841 (p90) REVERT: H 176 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8748 (mp0) REVERT: H 274 ASP cc_start: 0.8672 (t0) cc_final: 0.8375 (t0) REVERT: H 352 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8314 (tm-30) REVERT: H 395 GLU cc_start: 0.8525 (mp0) cc_final: 0.8231 (mp0) REVERT: H 416 SER cc_start: 0.8681 (p) cc_final: 0.8273 (m) REVERT: L 3 ASP cc_start: 0.8795 (t0) cc_final: 0.8235 (p0) outliers start: 238 outliers final: 178 residues processed: 1035 average time/residue: 0.4099 time to fit residues: 697.8939 Evaluate side-chains 1071 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 870 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET 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 343 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 322 ARG 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 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 369 ASN Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 60 THR 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 163 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 454 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 6 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 225 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 257 optimal weight: 0.3980 chunk 186 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN B 469 GLN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS E 93 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 469 GLN F 202 GLN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32282 Z= 0.212 Angle : 0.710 11.259 43824 Z= 0.342 Chirality : 0.047 0.264 4992 Planarity : 0.004 0.049 5454 Dihedral : 14.950 170.002 5363 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 6.91 % Allowed : 26.25 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.13), residues: 3968 helix: -0.86 (0.14), residues: 1334 sheet: -1.76 (0.22), residues: 520 loop : -1.58 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 504 PHE 0.020 0.001 PHE F 165 TYR 0.023 0.001 TYR D 110 ARG 0.013 0.000 ARG E 203 *********************** 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 1142 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 916 time to evaluate : 3.996 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 95 CYS cc_start: 0.8365 (p) cc_final: 0.8137 (p) REVERT: A 103 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8298 (mp0) REVERT: A 132 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8659 (tp30) REVERT: A 165 PHE cc_start: 0.8364 (p90) cc_final: 0.7712 (p90) REVERT: A 176 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8814 (tm-30) REVERT: A 179 MET cc_start: 0.7343 (ttp) cc_final: 0.6801 (tmm) REVERT: A 196 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8822 (pm20) REVERT: A 206 LYS cc_start: 0.8317 (tppp) cc_final: 0.7874 (tppp) REVERT: A 232 ASP cc_start: 0.8942 (t70) cc_final: 0.8621 (t70) REVERT: A 235 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7881 (pp) REVERT: A 309 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: A 311 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8653 (ttpp) REVERT: A 343 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: A 395 GLU cc_start: 0.8577 (mp0) cc_final: 0.8299 (mp0) REVERT: A 448 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: A 478 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8675 (pp30) REVERT: A 512 ARG cc_start: 0.7883 (tmt90) cc_final: 0.6682 (tmt90) REVERT: B 16 ASP cc_start: 0.8326 (t0) cc_final: 0.8038 (t0) REVERT: B 129 ASP cc_start: 0.9055 (m-30) cc_final: 0.8355 (m-30) REVERT: B 132 GLU cc_start: 0.8983 (pp20) cc_final: 0.8684 (pp20) REVERT: B 149 ARG cc_start: 0.8846 (mpp80) cc_final: 0.8279 (mpp80) REVERT: B 185 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8465 (mt) REVERT: B 199 GLU cc_start: 0.8246 (pp20) cc_final: 0.7769 (pp20) REVERT: B 206 LYS cc_start: 0.8962 (tptm) cc_final: 0.8604 (tptp) REVERT: B 269 ASP cc_start: 0.7893 (m-30) cc_final: 0.7576 (m-30) REVERT: B 286 MET cc_start: 0.8948 (tpp) cc_final: 0.8704 (tpp) REVERT: B 332 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.6954 (tp) REVERT: B 364 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7776 (t0) REVERT: B 469 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8966 (tt0) REVERT: B 483 MET cc_start: 0.9178 (tmm) cc_final: 0.8818 (tmm) REVERT: B 491 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: B 492 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7016 (mtpp) REVERT: B 495 SER cc_start: 0.9398 (m) cc_final: 0.9085 (p) REVERT: C 103 GLU cc_start: 0.8667 (mp0) cc_final: 0.8246 (mp0) REVERT: C 111 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7506 (mt-10) REVERT: C 179 MET cc_start: 0.5997 (pp-130) cc_final: 0.4923 (pp-130) REVERT: C 204 SER cc_start: 0.8233 (t) cc_final: 0.7806 (p) REVERT: C 452 SER cc_start: 0.9272 (p) cc_final: 0.8981 (m) REVERT: C 483 MET cc_start: 0.9515 (tmm) cc_final: 0.9166 (tmm) REVERT: C 500 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8363 (tm-30) REVERT: C 512 ARG cc_start: 0.8843 (mtp-110) cc_final: 0.8407 (mtm-85) REVERT: D 15 ASP cc_start: 0.7901 (p0) cc_final: 0.7650 (p0) REVERT: D 103 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8572 (mp0) REVERT: D 112 GLN cc_start: 0.7488 (mp10) cc_final: 0.7065 (mp-120) REVERT: D 131 PHE cc_start: 0.8521 (m-10) cc_final: 0.8230 (m-80) REVERT: D 215 ASP cc_start: 0.8446 (t0) cc_final: 0.8215 (t0) REVERT: D 269 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7812 (p0) REVERT: D 277 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7826 (tm-30) REVERT: D 291 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8534 (mmmt) REVERT: D 332 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8707 (pp) REVERT: D 334 GLN cc_start: 0.9088 (mt0) cc_final: 0.8814 (mt0) REVERT: D 352 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7932 (tm-30) REVERT: D 385 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8427 (ttp) REVERT: D 483 MET cc_start: 0.9295 (tmm) cc_final: 0.8629 (tmm) REVERT: E 132 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8704 (tp30) REVERT: E 134 LYS cc_start: 0.9358 (tmmm) cc_final: 0.9129 (tptm) REVERT: E 206 LYS cc_start: 0.8864 (tppp) cc_final: 0.8583 (tppt) REVERT: E 231 ARG cc_start: 0.9067 (ttp80) cc_final: 0.8775 (tmm-80) REVERT: E 235 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8398 (pp) REVERT: E 263 LEU cc_start: 0.9208 (mp) cc_final: 0.8925 (mp) REVERT: E 277 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7880 (tm-30) REVERT: E 332 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8601 (pp) REVERT: E 403 SER cc_start: 0.8733 (t) cc_final: 0.8309 (p) REVERT: E 404 ASP cc_start: 0.8341 (t0) cc_final: 0.7874 (t0) REVERT: E 406 ILE cc_start: 0.8692 (mp) cc_final: 0.8401 (mp) REVERT: E 448 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: E 512 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7599 (ttp80) REVERT: F 34 ASP cc_start: 0.8655 (t70) cc_final: 0.8421 (t70) REVERT: F 111 GLU cc_start: 0.7035 (pm20) cc_final: 0.6508 (pm20) REVERT: F 128 ARG cc_start: 0.8458 (mpt180) cc_final: 0.7998 (mmt-90) REVERT: F 132 GLU cc_start: 0.8792 (pp20) cc_final: 0.8499 (pp20) REVERT: F 161 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8197 (mtt90) REVERT: F 164 ASP cc_start: 0.7370 (t70) cc_final: 0.7152 (t70) REVERT: F 185 LEU cc_start: 0.8766 (mt) cc_final: 0.8136 (mt) REVERT: F 203 ARG cc_start: 0.8809 (mtm110) cc_final: 0.8349 (mtm110) REVERT: F 206 LYS cc_start: 0.9247 (tppt) cc_final: 0.8928 (tppp) REVERT: F 228 LYS cc_start: 0.9268 (mtpt) cc_final: 0.8635 (mtpp) REVERT: F 232 ASP cc_start: 0.8322 (m-30) cc_final: 0.7930 (m-30) REVERT: F 312 ASN cc_start: 0.9188 (t0) cc_final: 0.8615 (t0) REVERT: F 319 ASP cc_start: 0.7743 (t0) cc_final: 0.7252 (t0) REVERT: F 332 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7707 (pp) REVERT: F 334 GLN cc_start: 0.8389 (pp30) cc_final: 0.7903 (pp30) REVERT: F 483 MET cc_start: 0.9384 (tmm) cc_final: 0.9149 (tmm) REVERT: G 108 LYS cc_start: 0.8715 (tppp) cc_final: 0.8433 (tppt) REVERT: G 179 MET cc_start: 0.4956 (pp-130) cc_final: 0.4679 (pp-130) REVERT: G 258 TYR cc_start: 0.9162 (t80) cc_final: 0.8929 (t80) REVERT: G 343 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: G 465 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8560 (mm-40) REVERT: G 478 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7927 (tm-30) REVERT: G 483 MET cc_start: 0.9475 (tmm) cc_final: 0.9090 (tmm) REVERT: G 512 ARG cc_start: 0.8743 (mtp-110) cc_final: 0.8422 (ttp-110) REVERT: H 15 ASP cc_start: 0.8047 (p0) cc_final: 0.7760 (p0) REVERT: H 16 ASP cc_start: 0.8245 (t70) cc_final: 0.7919 (t70) REVERT: H 75 GLU cc_start: 0.7783 (tp30) cc_final: 0.7419 (tp30) REVERT: H 78 MET cc_start: 0.9517 (tpp) cc_final: 0.8943 (tpp) REVERT: H 82 MET cc_start: 0.8763 (mtm) cc_final: 0.8095 (mtm) REVERT: H 103 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: H 165 PHE cc_start: 0.8123 (p90) cc_final: 0.7846 (p90) REVERT: H 176 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8651 (mp0) REVERT: H 274 ASP cc_start: 0.8652 (t0) cc_final: 0.8387 (t0) REVERT: H 277 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7878 (tm-30) REVERT: H 352 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8328 (tm-30) REVERT: H 416 SER cc_start: 0.8613 (p) cc_final: 0.8230 (m) REVERT: L 3 ASP cc_start: 0.8783 (t0) cc_final: 0.8198 (p0) outliers start: 226 outliers final: 168 residues processed: 1029 average time/residue: 0.4012 time to fit residues: 678.5790 Evaluate side-chains 1081 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 886 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 235 LEU 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 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 369 ASN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 60 THR 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 163 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 454 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain O residue 3 ASP Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 6 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.9980 chunk 361 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 352 optimal weight: 0.0040 chunk 211 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 276 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 318 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 350 optimal weight: 10.0000 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 454 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** 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 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS ** G 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32282 Z= 0.207 Angle : 0.717 12.222 43824 Z= 0.344 Chirality : 0.047 0.276 4992 Planarity : 0.004 0.050 5454 Dihedral : 14.753 172.364 5363 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 6.66 % Allowed : 26.44 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 3968 helix: -0.90 (0.14), residues: 1365 sheet: -1.72 (0.22), residues: 520 loop : -1.62 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 93 PHE 0.020 0.001 PHE F 165 TYR 0.022 0.001 TYR C 258 ARG 0.014 0.000 ARG E 203 *********************** 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 1147 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 929 time to evaluate : 3.692 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 75 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7939 (mm-30) REVERT: A 92 HIS cc_start: 0.9273 (p90) cc_final: 0.9004 (p-80) REVERT: A 95 CYS cc_start: 0.8321 (p) cc_final: 0.8080 (p) REVERT: A 103 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: A 132 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8658 (tp30) REVERT: A 165 PHE cc_start: 0.8346 (p90) cc_final: 0.7661 (p90) REVERT: A 176 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8839 (tm-30) REVERT: A 196 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8870 (pm20) REVERT: A 206 LYS cc_start: 0.8376 (tppp) cc_final: 0.7933 (tppp) REVERT: A 235 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8016 (pp) REVERT: A 309 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: A 311 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8673 (ttpp) REVERT: A 343 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: A 395 GLU cc_start: 0.8572 (mp0) cc_final: 0.8310 (mp0) REVERT: A 448 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8288 (pt0) REVERT: A 478 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8654 (pp30) REVERT: A 512 ARG cc_start: 0.7879 (tmt90) cc_final: 0.6688 (tmt90) REVERT: B 16 ASP cc_start: 0.8347 (t0) cc_final: 0.8071 (t0) REVERT: B 129 ASP cc_start: 0.9057 (m-30) cc_final: 0.8336 (m-30) REVERT: B 132 GLU cc_start: 0.8986 (pp20) cc_final: 0.8769 (pp20) REVERT: B 149 ARG cc_start: 0.8873 (mpp80) cc_final: 0.8276 (mpp80) REVERT: B 199 GLU cc_start: 0.8273 (pp20) cc_final: 0.7800 (pp20) REVERT: B 203 ARG cc_start: 0.8708 (ptp-110) cc_final: 0.8285 (mtm110) REVERT: B 206 LYS cc_start: 0.8976 (tptm) cc_final: 0.8632 (tptp) REVERT: B 269 ASP cc_start: 0.7850 (m-30) cc_final: 0.7551 (m-30) REVERT: B 286 MET cc_start: 0.8934 (tpp) cc_final: 0.8691 (tpp) REVERT: B 332 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.6812 (tp) REVERT: B 364 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7722 (t0) REVERT: B 483 MET cc_start: 0.9188 (tmm) cc_final: 0.8865 (tmm) REVERT: B 491 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: B 492 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.6970 (mtpp) REVERT: B 495 SER cc_start: 0.9402 (m) cc_final: 0.9079 (p) REVERT: C 111 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7521 (mt-10) REVERT: C 179 MET cc_start: 0.5970 (pp-130) cc_final: 0.4861 (pp-130) REVERT: C 204 SER cc_start: 0.8251 (t) cc_final: 0.7827 (p) REVERT: C 452 SER cc_start: 0.9264 (p) cc_final: 0.9010 (m) REVERT: C 483 MET cc_start: 0.9518 (tmm) cc_final: 0.9178 (tmm) REVERT: C 500 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 512 ARG cc_start: 0.8833 (mtp-110) cc_final: 0.8415 (mtm-85) REVERT: D 15 ASP cc_start: 0.7964 (p0) cc_final: 0.7710 (p0) REVERT: D 75 GLU cc_start: 0.7805 (tp30) cc_final: 0.7250 (tp30) REVERT: D 103 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: D 112 GLN cc_start: 0.7451 (mp10) cc_final: 0.6983 (mp-120) REVERT: D 131 PHE cc_start: 0.8453 (m-10) cc_final: 0.8165 (m-80) REVERT: D 215 ASP cc_start: 0.8441 (t0) cc_final: 0.8211 (t0) REVERT: D 269 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7799 (p0) REVERT: D 277 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7776 (tm-30) REVERT: D 291 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8614 (mmmt) REVERT: D 332 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8708 (pp) REVERT: D 334 GLN cc_start: 0.9088 (mt0) cc_final: 0.8808 (mt0) REVERT: D 352 GLU cc_start: 0.8583 (tm-30) cc_final: 0.7898 (tm-30) REVERT: D 385 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8459 (ttp) REVERT: D 483 MET cc_start: 0.9310 (tmm) cc_final: 0.8640 (tmm) REVERT: E 132 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8721 (tp30) REVERT: E 134 LYS cc_start: 0.9350 (tmmm) cc_final: 0.9132 (tptm) REVERT: E 203 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8373 (mtm110) REVERT: E 206 LYS cc_start: 0.8897 (tppp) cc_final: 0.8623 (tppt) REVERT: E 231 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8787 (tmm-80) REVERT: E 235 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8369 (pp) REVERT: E 263 LEU cc_start: 0.9200 (mp) cc_final: 0.8918 (mp) REVERT: E 277 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7858 (tm-30) REVERT: E 332 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8604 (pp) REVERT: E 403 SER cc_start: 0.8767 (t) cc_final: 0.8358 (p) REVERT: E 404 ASP cc_start: 0.8321 (t0) cc_final: 0.7859 (t0) REVERT: E 406 ILE cc_start: 0.8680 (mp) cc_final: 0.8395 (mp) REVERT: E 448 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: E 512 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7588 (ttp80) REVERT: F 34 ASP cc_start: 0.8643 (t70) cc_final: 0.8420 (t70) REVERT: F 132 GLU cc_start: 0.8776 (pp20) cc_final: 0.8484 (pp20) REVERT: F 161 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8080 (mtt90) REVERT: F 185 LEU cc_start: 0.8768 (mt) cc_final: 0.8158 (mt) REVERT: F 203 ARG cc_start: 0.8790 (mtm110) cc_final: 0.8381 (mtm110) REVERT: F 205 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8710 (mttm) REVERT: F 206 LYS cc_start: 0.9251 (tppt) cc_final: 0.8788 (tppp) REVERT: F 228 LYS cc_start: 0.9247 (mtpt) cc_final: 0.8628 (mtpp) REVERT: F 232 ASP cc_start: 0.8329 (m-30) cc_final: 0.7962 (m-30) REVERT: F 312 ASN cc_start: 0.9196 (t0) cc_final: 0.8621 (t0) REVERT: F 319 ASP cc_start: 0.7747 (t0) cc_final: 0.7198 (t0) REVERT: F 332 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.6968 (tp) REVERT: F 334 GLN cc_start: 0.8328 (pp30) cc_final: 0.7860 (pp30) REVERT: F 483 MET cc_start: 0.9384 (tmm) cc_final: 0.9144 (tmm) REVERT: G 108 LYS cc_start: 0.8676 (tppp) cc_final: 0.8402 (tppt) REVERT: G 179 MET cc_start: 0.4941 (pp-130) cc_final: 0.4671 (pp-130) REVERT: G 343 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: G 465 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8575 (mm-40) REVERT: G 478 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: G 483 MET cc_start: 0.9440 (tmm) cc_final: 0.8918 (tmm) REVERT: G 488 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8833 (tp) REVERT: G 512 ARG cc_start: 0.8742 (mtp-110) cc_final: 0.8429 (ttp-110) REVERT: H 15 ASP cc_start: 0.8041 (p0) cc_final: 0.7760 (p0) REVERT: H 16 ASP cc_start: 0.8237 (t70) cc_final: 0.7898 (t70) REVERT: H 75 GLU cc_start: 0.7809 (tp30) cc_final: 0.7389 (tp30) REVERT: H 78 MET cc_start: 0.9497 (tpp) cc_final: 0.9145 (tpp) REVERT: H 82 MET cc_start: 0.8663 (mtm) cc_final: 0.8330 (mtm) REVERT: H 93 HIS cc_start: 0.8752 (p-80) cc_final: 0.8384 (p90) REVERT: H 103 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: H 165 PHE cc_start: 0.8101 (p90) cc_final: 0.7816 (p90) REVERT: H 176 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8700 (mp0) REVERT: H 274 ASP cc_start: 0.8662 (t0) cc_final: 0.8341 (t0) REVERT: H 277 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7882 (tm-30) REVERT: H 334 GLN cc_start: 0.9083 (mt0) cc_final: 0.8774 (mt0) REVERT: H 352 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8361 (tm-30) REVERT: H 416 SER cc_start: 0.8679 (p) cc_final: 0.8255 (m) REVERT: K 1 MET cc_start: 0.5968 (tpp) cc_final: 0.5693 (tpp) REVERT: L 3 ASP cc_start: 0.8790 (t0) cc_final: 0.8201 (p0) outliers start: 218 outliers final: 169 residues processed: 1039 average time/residue: 0.3910 time to fit residues: 671.4147 Evaluate side-chains 1086 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 890 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 235 LEU 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 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 369 ASN Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 53 SER 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 163 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 367 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 478 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 454 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.9990 chunk 372 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 390 optimal weight: 7.9990 chunk 359 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 454 HIS D 93 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS ** G 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN ** H 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 32282 Z= 0.413 Angle : 0.805 12.204 43824 Z= 0.396 Chirality : 0.050 0.295 4992 Planarity : 0.004 0.057 5454 Dihedral : 14.795 169.378 5363 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 6.48 % Allowed : 26.68 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.21 (0.13), residues: 3968 helix: -0.99 (0.14), residues: 1369 sheet: -1.80 (0.22), residues: 520 loop : -1.66 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 504 PHE 0.021 0.002 PHE F 165 TYR 0.025 0.002 TYR P 12 ARG 0.013 0.001 ARG E 203 ********************** 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 1093 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 881 time to evaluate : 3.658 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 95 CYS cc_start: 0.8238 (p) cc_final: 0.7948 (p) REVERT: A 103 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: A 132 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8730 (tp30) REVERT: A 165 PHE cc_start: 0.8426 (p90) cc_final: 0.7733 (p90) REVERT: A 176 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8896 (tm-30) REVERT: A 196 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8835 (pm20) REVERT: A 206 LYS cc_start: 0.8633 (tppp) cc_final: 0.8131 (tppp) REVERT: A 232 ASP cc_start: 0.8985 (t70) cc_final: 0.8684 (t70) REVERT: A 235 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8195 (pp) REVERT: A 311 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8660 (ttpp) REVERT: A 395 GLU cc_start: 0.8635 (mp0) cc_final: 0.8333 (mp0) REVERT: A 448 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: A 498 GLN cc_start: 0.9049 (pt0) cc_final: 0.8599 (pt0) REVERT: A 506 LEU cc_start: 0.9214 (mm) cc_final: 0.8990 (mm) REVERT: A 512 ARG cc_start: 0.7869 (tmt90) cc_final: 0.6617 (tmt90) REVERT: B 129 ASP cc_start: 0.9053 (m-30) cc_final: 0.8363 (m-30) REVERT: B 132 GLU cc_start: 0.8991 (pp20) cc_final: 0.8689 (pp20) REVERT: B 149 ARG cc_start: 0.8874 (mpp80) cc_final: 0.8290 (mpp80) REVERT: B 199 GLU cc_start: 0.8314 (pp20) cc_final: 0.7937 (pp20) REVERT: B 206 LYS cc_start: 0.8996 (tptm) cc_final: 0.8764 (mmmt) REVERT: B 269 ASP cc_start: 0.8011 (m-30) cc_final: 0.7700 (m-30) REVERT: B 286 MET cc_start: 0.9050 (tpp) cc_final: 0.8795 (tpp) REVERT: B 332 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7024 (tp) REVERT: B 495 SER cc_start: 0.9448 (m) cc_final: 0.9136 (p) REVERT: C 111 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7527 (mt-10) REVERT: C 179 MET cc_start: 0.6122 (pp-130) cc_final: 0.5067 (pp-130) REVERT: C 204 SER cc_start: 0.8233 (t) cc_final: 0.7801 (p) REVERT: C 277 GLN cc_start: 0.9199 (pp30) cc_final: 0.8703 (pp30) REVERT: C 452 SER cc_start: 0.9313 (p) cc_final: 0.9018 (m) REVERT: C 483 MET cc_start: 0.9552 (tmm) cc_final: 0.9142 (tmm) REVERT: C 512 ARG cc_start: 0.8886 (mtp-110) cc_final: 0.8429 (mtm-85) REVERT: D 15 ASP cc_start: 0.7957 (p0) cc_final: 0.7720 (p0) REVERT: D 103 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8577 (mp0) REVERT: D 112 GLN cc_start: 0.7679 (mp10) cc_final: 0.7195 (mp-120) REVERT: D 131 PHE cc_start: 0.8470 (m-10) cc_final: 0.8193 (m-80) REVERT: D 215 ASP cc_start: 0.8552 (t0) cc_final: 0.8333 (t0) REVERT: D 277 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7965 (tm-30) REVERT: D 291 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8626 (mmmt) REVERT: D 332 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8682 (pp) REVERT: D 352 GLU cc_start: 0.8752 (tm-30) cc_final: 0.7990 (tm-30) REVERT: D 483 MET cc_start: 0.9332 (tmm) cc_final: 0.8645 (tmm) REVERT: E 56 THR cc_start: 0.9272 (p) cc_final: 0.9039 (t) REVERT: E 132 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8771 (tp30) REVERT: E 134 LYS cc_start: 0.9350 (tmmm) cc_final: 0.9140 (tptm) REVERT: E 203 ARG cc_start: 0.8799 (mtm110) cc_final: 0.8397 (mtm110) REVERT: E 206 LYS cc_start: 0.9017 (tppp) cc_final: 0.8579 (tppp) REVERT: E 231 ARG cc_start: 0.9133 (ttp80) cc_final: 0.8790 (tmm-80) REVERT: E 235 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8395 (pp) REVERT: E 263 LEU cc_start: 0.9292 (mp) cc_final: 0.9038 (mp) REVERT: E 277 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8055 (tm-30) REVERT: E 403 SER cc_start: 0.8737 (t) cc_final: 0.8305 (p) REVERT: E 404 ASP cc_start: 0.8305 (t0) cc_final: 0.7921 (t0) REVERT: E 406 ILE cc_start: 0.8767 (mp) cc_final: 0.8523 (mp) REVERT: E 448 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: F 34 ASP cc_start: 0.8800 (t70) cc_final: 0.8577 (t70) REVERT: F 128 ARG cc_start: 0.8257 (mpt180) cc_final: 0.7881 (mmt-90) REVERT: F 132 GLU cc_start: 0.8799 (pp20) cc_final: 0.8518 (pp20) REVERT: F 185 LEU cc_start: 0.8862 (mt) cc_final: 0.8264 (mt) REVERT: F 203 ARG cc_start: 0.8824 (mtm110) cc_final: 0.8467 (mtm110) REVERT: F 205 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8653 (mtpp) REVERT: F 206 LYS cc_start: 0.9279 (tppt) cc_final: 0.8932 (tppp) REVERT: F 228 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8608 (mtpp) REVERT: F 232 ASP cc_start: 0.8311 (m-30) cc_final: 0.7951 (m-30) REVERT: F 306 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8929 (t) REVERT: F 319 ASP cc_start: 0.7713 (t0) cc_final: 0.7185 (t0) REVERT: F 332 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7799 (pp) REVERT: F 334 GLN cc_start: 0.8214 (pp30) cc_final: 0.7859 (pp30) REVERT: F 352 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8593 (tm-30) REVERT: F 418 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8083 (p0) REVERT: F 483 MET cc_start: 0.9371 (tmm) cc_final: 0.9160 (tmm) REVERT: G 108 LYS cc_start: 0.8872 (tppp) cc_final: 0.8543 (tppt) REVERT: G 343 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: G 409 LYS cc_start: 0.8303 (ttmm) cc_final: 0.8028 (ttmm) REVERT: G 465 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8641 (mm-40) REVERT: G 483 MET cc_start: 0.9409 (tmm) cc_final: 0.8808 (tmm) REVERT: G 488 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8911 (tp) REVERT: G 512 ARG cc_start: 0.8825 (mtp-110) cc_final: 0.8383 (mtm-85) REVERT: H 15 ASP cc_start: 0.8126 (p0) cc_final: 0.7828 (p0) REVERT: H 16 ASP cc_start: 0.8297 (t70) cc_final: 0.8016 (t0) REVERT: H 78 MET cc_start: 0.9520 (tpp) cc_final: 0.9125 (tpp) REVERT: H 82 MET cc_start: 0.8909 (mtm) cc_final: 0.8474 (mtm) REVERT: H 103 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (mp0) REVERT: H 165 PHE cc_start: 0.8038 (p90) cc_final: 0.7724 (p90) REVERT: H 274 ASP cc_start: 0.8683 (t0) cc_final: 0.8328 (t0) REVERT: H 277 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7930 (tm-30) REVERT: H 318 VAL cc_start: 0.9662 (t) cc_final: 0.9434 (p) REVERT: H 352 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8374 (tm-30) REVERT: H 416 SER cc_start: 0.8896 (p) cc_final: 0.8514 (m) REVERT: K 1 MET cc_start: 0.6035 (tpp) cc_final: 0.5761 (tpp) REVERT: L 3 ASP cc_start: 0.8794 (t0) cc_final: 0.8189 (p0) outliers start: 212 outliers final: 173 residues processed: 993 average time/residue: 0.3847 time to fit residues: 629.4619 Evaluate side-chains 1038 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 847 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 466 HIS Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 343 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 335 GLU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 490 PHE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 478 GLN Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 369 ASN Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 60 THR 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 163 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 343 GLN Chi-restraints excluded: chain G residue 373 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 465 GLN Chi-restraints excluded: chain G residue 488 LEU Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 454 HIS Chi-restraints excluded: chain H residue 467 SER Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain N residue 6 ILE Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.3980 chunk 331 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 311 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 319 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 454 HIS C 498 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.148916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105432 restraints weight = 50272.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109796 restraints weight = 23770.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112600 restraints weight = 14693.375| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32282 Z= 0.206 Angle : 0.746 12.281 43824 Z= 0.359 Chirality : 0.047 0.270 4992 Planarity : 0.004 0.050 5454 Dihedral : 14.391 167.238 5363 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 6.05 % Allowed : 27.29 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.09 (0.13), residues: 3968 helix: -0.88 (0.14), residues: 1353 sheet: -1.74 (0.22), residues: 520 loop : -1.60 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 137 PHE 0.020 0.001 PHE F 165 TYR 0.023 0.001 TYR C 258 ARG 0.013 0.001 ARG E 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10410.06 seconds wall clock time: 187 minutes 5.53 seconds (11225.53 seconds total)