Starting phenix.real_space_refine on Fri Oct 11 09:03:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pex_17640/10_2024/8pex_17640.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pex_17640/10_2024/8pex_17640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pex_17640/10_2024/8pex_17640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pex_17640/10_2024/8pex_17640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pex_17640/10_2024/8pex_17640.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pex_17640/10_2024/8pex_17640.cif" } resolution = 3.1 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= 0.010 sd= 0.057 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 266 5.16 5 C 34130 2.51 5 N 9882 2.21 5 O 10425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 54751 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "B" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "C" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "D" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "E" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "F" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "I" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "J" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "K" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "L" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "M" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "N" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3299 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 401} Chain: "a" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "b" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "c" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "d" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "e" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "f" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "g" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "h" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "i" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "j" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 24.10, per 1000 atoms: 0.44 Number of scatterers: 54751 At special positions: 0 Unit cell: (171.392, 178.048, 237.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 266 16.00 P 36 15.00 Mg 12 11.99 O 10425 8.00 N 9882 7.00 C 34130 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 - 3.00 Amino acid : True - 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: 11.07 Conformation dependent library (CDL) restraints added in 5.5 seconds 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12960 Finding SS restraints... Secondary structure from input PDB file: 283 helices and 40 sheets defined 59.0% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 4.284A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.639A pdb=" N ASN A 135 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.735A pdb=" N ARG A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.598A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.701A pdb=" N LEU A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 347 through 353 Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.683A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 418 removed outlier: 3.501A pdb=" N ARG A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 removed outlier: 3.558A pdb=" N THR B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.595A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.805A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.994A pdb=" N ASN B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.662A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.561A pdb=" N ARG B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 255 Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.535A pdb=" N ALA B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.861A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 405 Processing helix chain 'B' and resid 408 through 418 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.848A pdb=" N THR C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 removed outlier: 3.573A pdb=" N SER C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.542A pdb=" N ILE C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.741A pdb=" N ASN C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.239A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.509A pdb=" N ARG C 299 " --> pdb=" O HIS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 333 removed outlier: 4.201A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.647A pdb=" N ALA C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.834A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 123 through 129 removed outlier: 3.596A pdb=" N ARG D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.874A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 235 through 255 Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.893A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.564A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.646A pdb=" N LEU D 370 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'D' and resid 391 through 406 Processing helix chain 'D' and resid 408 through 419 Processing helix chain 'E' and resid 2 through 8 removed outlier: 3.725A pdb=" N LEU E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 22 Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.685A pdb=" N GLY E 46 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 removed outlier: 3.621A pdb=" N SER E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.551A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 129 removed outlier: 4.060A pdb=" N ASN E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.524A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 221 removed outlier: 3.733A pdb=" N VAL E 216 " --> pdb=" O ARG E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.726A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 325 through 335 removed outlier: 3.814A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.659A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.957A pdb=" N MET E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 419 Processing helix chain 'F' and resid 2 through 7 removed outlier: 4.744A pdb=" N LEU F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 7 " --> pdb=" O LEU F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 7' Processing helix chain 'F' and resid 10 through 20 Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 82 through 89 removed outlier: 3.896A pdb=" N PHE F 89 " --> pdb=" O GLN F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 235 through 255 removed outlier: 3.910A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 285 through 289 removed outlier: 3.837A pdb=" N VAL F 289 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 302 removed outlier: 4.055A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 325 through 336 removed outlier: 4.429A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 removed outlier: 4.346A pdb=" N ALA F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU F 351 " --> pdb=" O ARG F 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 346 through 351' Processing helix chain 'F' and resid 367 through 372 removed outlier: 4.100A pdb=" N LEU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 367 through 372' Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 391 through 406 removed outlier: 3.815A pdb=" N THR F 406 " --> pdb=" O LYS F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 418 Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 10 through 22 removed outlier: 4.163A pdb=" N THR I 16 " --> pdb=" O SER I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 46 removed outlier: 4.457A pdb=" N ILE I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA I 43 " --> pdb=" O LEU I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 71 removed outlier: 3.564A pdb=" N SER I 71 " --> pdb=" O ALA I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 89 removed outlier: 3.566A pdb=" N PHE I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 130 removed outlier: 3.874A pdb=" N ASN I 129 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS I 130 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 136 Processing helix chain 'I' and resid 153 through 166 Processing helix chain 'I' and resid 183 through 199 Processing helix chain 'I' and resid 212 through 223 removed outlier: 3.550A pdb=" N VAL I 223 " --> pdb=" O MET I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 256 removed outlier: 3.791A pdb=" N HIS I 239 " --> pdb=" O PRO I 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS I 256 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 278 Processing helix chain 'I' and resid 290 through 304 Proline residue: I 297 - end of helix removed outlier: 3.674A pdb=" N PHE I 300 " --> pdb=" O ARG I 296 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA I 304 " --> pdb=" O PHE I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 335 removed outlier: 4.120A pdb=" N GLU I 329 " --> pdb=" O SER I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 352 removed outlier: 3.692A pdb=" N ALA I 350 " --> pdb=" O SER I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 388 Processing helix chain 'I' and resid 391 through 406 removed outlier: 3.989A pdb=" N GLU I 397 " --> pdb=" O ILE I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 419 Processing helix chain 'J' and resid 3 through 9 Processing helix chain 'J' and resid 10 through 22 Processing helix chain 'J' and resid 30 through 44 Processing helix chain 'J' and resid 82 through 90 Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'J' and resid 155 through 166 removed outlier: 3.936A pdb=" N ALA J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 199 Processing helix chain 'J' and resid 212 through 223 Processing helix chain 'J' and resid 235 through 255 removed outlier: 3.518A pdb=" N HIS J 239 " --> pdb=" O PRO J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 278 Processing helix chain 'J' and resid 294 through 303 Processing helix chain 'J' and resid 325 through 335 Processing helix chain 'J' and resid 346 through 351 removed outlier: 3.883A pdb=" N ALA J 350 " --> pdb=" O SER J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 372 removed outlier: 3.730A pdb=" N LEU J 370 " --> pdb=" O LYS J 367 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR J 372 " --> pdb=" O GLU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 388 removed outlier: 3.548A pdb=" N GLN J 378 " --> pdb=" O GLN J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 405 removed outlier: 4.138A pdb=" N MET J 405 " --> pdb=" O ASN J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 418 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 11 through 21 removed outlier: 3.923A pdb=" N ILE K 15 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR K 16 " --> pdb=" O SER K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 45 removed outlier: 3.616A pdb=" N SER K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 90 Processing helix chain 'K' and resid 123 through 129 removed outlier: 3.698A pdb=" N ASN K 129 " --> pdb=" O GLU K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 136 Processing helix chain 'K' and resid 155 through 166 removed outlier: 3.826A pdb=" N ALA K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 199 Processing helix chain 'K' and resid 212 through 221 removed outlier: 3.582A pdb=" N ARG K 221 " --> pdb=" O THR K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 255 Processing helix chain 'K' and resid 266 through 278 Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 325 through 335 Processing helix chain 'K' and resid 346 through 352 removed outlier: 3.590A pdb=" N ALA K 350 " --> pdb=" O SER K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 372 removed outlier: 3.539A pdb=" N THR K 372 " --> pdb=" O GLU K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 373 through 388 Processing helix chain 'K' and resid 391 through 406 Processing helix chain 'K' and resid 408 through 419 removed outlier: 3.847A pdb=" N SER K 419 " --> pdb=" O MET K 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 8 removed outlier: 3.641A pdb=" N LEU L 6 " --> pdb=" O ASN L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 22 Processing helix chain 'L' and resid 30 through 46 Processing helix chain 'L' and resid 82 through 90 removed outlier: 3.663A pdb=" N ILE L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 132 through 136 Processing helix chain 'L' and resid 156 through 166 Processing helix chain 'L' and resid 183 through 199 Processing helix chain 'L' and resid 212 through 221 removed outlier: 3.744A pdb=" N ARG L 221 " --> pdb=" O THR L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 255 removed outlier: 3.683A pdb=" N HIS L 239 " --> pdb=" O PRO L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 278 Processing helix chain 'L' and resid 291 through 293 No H-bonds generated for 'chain 'L' and resid 291 through 293' Processing helix chain 'L' and resid 294 through 302 removed outlier: 3.536A pdb=" N LYS L 298 " --> pdb=" O LEU L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 335 removed outlier: 3.633A pdb=" N GLU L 329 " --> pdb=" O SER L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 352 Processing helix chain 'L' and resid 367 through 372 removed outlier: 3.856A pdb=" N LEU L 371 " --> pdb=" O LYS L 367 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR L 372 " --> pdb=" O GLU L 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 367 through 372' Processing helix chain 'L' and resid 373 through 388 removed outlier: 3.588A pdb=" N LEU L 377 " --> pdb=" O THR L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 405 removed outlier: 3.967A pdb=" N MET L 405 " --> pdb=" O ASN L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 408 through 419 Processing helix chain 'M' and resid 3 through 9 removed outlier: 3.639A pdb=" N THR M 9 " --> pdb=" O GLU M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 22 Processing helix chain 'M' and resid 30 through 46 removed outlier: 3.641A pdb=" N ILE M 34 " --> pdb=" O ARG M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 71 removed outlier: 3.668A pdb=" N SER M 71 " --> pdb=" O ALA M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 90 Processing helix chain 'M' and resid 123 through 129 removed outlier: 3.540A pdb=" N ARG M 128 " --> pdb=" O PRO M 124 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN M 129 " --> pdb=" O GLU M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 166 Processing helix chain 'M' and resid 183 through 199 Processing helix chain 'M' and resid 212 through 221 removed outlier: 3.702A pdb=" N ARG M 221 " --> pdb=" O THR M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 255 Processing helix chain 'M' and resid 266 through 278 Processing helix chain 'M' and resid 294 through 303 Processing helix chain 'M' and resid 325 through 335 removed outlier: 3.614A pdb=" N GLU M 329 " --> pdb=" O SER M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 352 removed outlier: 3.608A pdb=" N ALA M 350 " --> pdb=" O SER M 346 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS M 352 " --> pdb=" O LYS M 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 372 removed outlier: 3.873A pdb=" N LEU M 370 " --> pdb=" O LYS M 367 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR M 372 " --> pdb=" O GLU M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 391 through 406 removed outlier: 4.065A pdb=" N GLU M 397 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR M 406 " --> pdb=" O LYS M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 408 through 419 Processing helix chain 'N' and resid 2 through 8 removed outlier: 3.638A pdb=" N LEU N 6 " --> pdb=" O ASN N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 22 Processing helix chain 'N' and resid 30 through 46 removed outlier: 3.529A pdb=" N ILE N 34 " --> pdb=" O ARG N 30 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER N 45 " --> pdb=" O GLN N 41 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY N 46 " --> pdb=" O HIS N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 90 removed outlier: 3.789A pdb=" N ILE N 86 " --> pdb=" O SER N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 129 removed outlier: 3.961A pdb=" N ASN N 129 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 136 Processing helix chain 'N' and resid 155 through 166 removed outlier: 3.704A pdb=" N ALA N 159 " --> pdb=" O GLU N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 199 Processing helix chain 'N' and resid 212 through 221 Processing helix chain 'N' and resid 235 through 255 removed outlier: 3.716A pdb=" N HIS N 239 " --> pdb=" O PRO N 235 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 278 Processing helix chain 'N' and resid 291 through 293 No H-bonds generated for 'chain 'N' and resid 291 through 293' Processing helix chain 'N' and resid 294 through 303 removed outlier: 3.513A pdb=" N LYS N 298 " --> pdb=" O LEU N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 333 Processing helix chain 'N' and resid 367 through 372 removed outlier: 3.543A pdb=" N LEU N 370 " --> pdb=" O LYS N 367 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU N 371 " --> pdb=" O GLU N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 373 through 388 Processing helix chain 'N' and resid 391 through 406 removed outlier: 3.583A pdb=" N THR N 406 " --> pdb=" O LYS N 402 " (cutoff:3.500A) Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'a' and resid 5 through 40 Processing helix chain 'a' and resid 45 through 99 removed outlier: 6.483A pdb=" N THR a 94 " --> pdb=" O GLN a 90 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA a 95 " --> pdb=" O GLN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 110 removed outlier: 3.872A pdb=" N GLU a 103 " --> pdb=" O LEU a 100 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N MET a 105 " --> pdb=" O PRO a 102 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLY a 106 " --> pdb=" O GLU a 103 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER a 108 " --> pdb=" O MET a 105 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU a 110 " --> pdb=" O TYR a 107 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 135 removed outlier: 3.542A pdb=" N ALA a 135 " --> pdb=" O LEU a 131 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 154 removed outlier: 3.818A pdb=" N LEU a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 166 removed outlier: 3.734A pdb=" N VAL a 162 " --> pdb=" O ASP a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 190 removed outlier: 3.512A pdb=" N VAL a 190 " --> pdb=" O SER a 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 40 Processing helix chain 'b' and resid 44 through 100 removed outlier: 6.155A pdb=" N THR b 94 " --> pdb=" O GLN b 90 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA b 95 " --> pdb=" O GLN b 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 110 removed outlier: 4.088A pdb=" N GLU b 109 " --> pdb=" O MET b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 111 through 137 removed outlier: 3.682A pdb=" N ASP b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA b 125 " --> pdb=" O ARG b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 154 Processing helix chain 'b' and resid 159 through 164 removed outlier: 3.757A pdb=" N ASP b 164 " --> pdb=" O ALA b 160 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 190 Processing helix chain 'c' and resid 5 through 40 Processing helix chain 'c' and resid 44 through 100 removed outlier: 5.775A pdb=" N THR c 94 " --> pdb=" O GLN c 90 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA c 95 " --> pdb=" O GLN c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 109 removed outlier: 3.732A pdb=" N GLU c 109 " --> pdb=" O MET c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 137 Processing helix chain 'c' and resid 143 through 154 Processing helix chain 'c' and resid 158 through 164 removed outlier: 3.750A pdb=" N ASP c 164 " --> pdb=" O ALA c 160 " (cutoff:3.500A) Processing helix chain 'c' and resid 170 through 190 Processing helix chain 'd' and resid 5 through 40 Processing helix chain 'd' and resid 44 through 100 removed outlier: 6.265A pdb=" N THR d 94 " --> pdb=" O GLN d 90 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA d 95 " --> pdb=" O GLN d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 105 removed outlier: 3.905A pdb=" N LEU d 104 " --> pdb=" O LEU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 136 Processing helix chain 'd' and resid 146 through 153 removed outlier: 3.588A pdb=" N ILE d 153 " --> pdb=" O ILE d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 158 through 164 removed outlier: 3.917A pdb=" N ASP d 164 " --> pdb=" O ALA d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 190 Processing helix chain 'e' and resid 5 through 39 Processing helix chain 'e' and resid 44 through 100 removed outlier: 6.052A pdb=" N THR e 94 " --> pdb=" O GLN e 90 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA e 95 " --> pdb=" O GLN e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 100 through 105 removed outlier: 3.503A pdb=" N MET e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 136 removed outlier: 4.106A pdb=" N LYS e 136 " --> pdb=" O SER e 132 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 154 removed outlier: 3.531A pdb=" N LEU e 150 " --> pdb=" O ASP e 146 " (cutoff:3.500A) Processing helix chain 'e' and resid 158 through 163 removed outlier: 3.576A pdb=" N VAL e 162 " --> pdb=" O ASP e 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 170 through 190 removed outlier: 3.572A pdb=" N VAL e 190 " --> pdb=" O SER e 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 40 Processing helix chain 'f' and resid 44 through 101 removed outlier: 6.151A pdb=" N THR f 94 " --> pdb=" O GLN f 90 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA f 95 " --> pdb=" O GLN f 91 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 104 No H-bonds generated for 'chain 'f' and resid 102 through 104' Processing helix chain 'f' and resid 111 through 137 removed outlier: 3.806A pdb=" N GLY f 137 " --> pdb=" O TRP f 133 " (cutoff:3.500A) Processing helix chain 'f' and resid 146 through 153 removed outlier: 3.778A pdb=" N LEU f 150 " --> pdb=" O ASP f 146 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE f 153 " --> pdb=" O ILE f 149 " (cutoff:3.500A) Processing helix chain 'f' and resid 158 through 164 Processing helix chain 'f' and resid 170 through 190 Processing helix chain 'g' and resid 5 through 40 Processing helix chain 'g' and resid 44 through 100 removed outlier: 6.511A pdb=" N THR g 94 " --> pdb=" O GLN g 90 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA g 95 " --> pdb=" O GLN g 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 105 removed outlier: 3.756A pdb=" N MET g 105 " --> pdb=" O ALA g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 137 Processing helix chain 'g' and resid 146 through 153 removed outlier: 3.769A pdb=" N ILE g 153 " --> pdb=" O ILE g 149 " (cutoff:3.500A) Processing helix chain 'g' and resid 158 through 163 Processing helix chain 'g' and resid 170 through 190 Processing helix chain 'h' and resid 5 through 40 Processing helix chain 'h' and resid 44 through 101 removed outlier: 6.165A pdb=" N THR h 94 " --> pdb=" O GLN h 90 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA h 95 " --> pdb=" O GLN h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 104 No H-bonds generated for 'chain 'h' and resid 102 through 104' Processing helix chain 'h' and resid 111 through 136 removed outlier: 4.263A pdb=" N LYS h 136 " --> pdb=" O SER h 132 " (cutoff:3.500A) Processing helix chain 'h' and resid 146 through 154 removed outlier: 3.579A pdb=" N LEU h 150 " --> pdb=" O ASP h 146 " (cutoff:3.500A) Processing helix chain 'h' and resid 158 through 163 Processing helix chain 'h' and resid 170 through 190 Processing helix chain 'i' and resid 5 through 40 Processing helix chain 'i' and resid 44 through 101 removed outlier: 6.401A pdb=" N THR i 94 " --> pdb=" O GLN i 90 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA i 95 " --> pdb=" O GLN i 91 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 102 through 104 No H-bonds generated for 'chain 'i' and resid 102 through 104' Processing helix chain 'i' and resid 111 through 136 Processing helix chain 'i' and resid 146 through 154 removed outlier: 3.747A pdb=" N LEU i 150 " --> pdb=" O ASP i 146 " (cutoff:3.500A) Processing helix chain 'i' and resid 158 through 164 Processing helix chain 'i' and resid 170 through 190 Processing helix chain 'j' and resid 5 through 40 Processing helix chain 'j' and resid 44 through 92 Processing helix chain 'j' and resid 92 through 100 removed outlier: 3.745A pdb=" N LEU j 96 " --> pdb=" O HIS j 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 137 Processing helix chain 'j' and resid 146 through 154 Processing helix chain 'j' and resid 158 through 165 Processing helix chain 'j' and resid 170 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 102 removed outlier: 6.652A pdb=" N SER A 98 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 115 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG A 102 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU A 113 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 231 removed outlier: 7.454A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 261 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 209 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 316 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 262 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N THR A 318 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 264 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LEU A 320 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 364 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 81 removed outlier: 6.473A pdb=" N THR B 96 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL B 119 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER B 98 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS B 115 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG B 102 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU B 113 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 227 through 229 removed outlier: 7.832A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 227 through 229 removed outlier: 7.832A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG B 173 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 343 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 175 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA9, first strand: chain 'C' and resid 111 through 112 removed outlier: 6.367A pdb=" N THR C 96 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL C 119 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER C 98 " --> pdb=" O ASN C 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 227 through 231 removed outlier: 7.905A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER C 230 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 208 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE C 316 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE C 262 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR C 318 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU C 264 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N LEU C 320 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 227 through 231 removed outlier: 7.905A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER C 230 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 208 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE C 316 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE C 262 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR C 318 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU C 264 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N LEU C 320 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG C 173 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU C 343 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 284 through 285 removed outlier: 4.041A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 79 through 81 removed outlier: 4.862A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS D 100 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL D 116 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.773A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 262 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR D 318 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU D 264 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N LEU D 320 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL D 228 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL D 206 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER D 230 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D 208 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.773A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG D 173 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LEU D 343 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 81 removed outlier: 3.625A pdb=" N GLY E 99 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 227 through 229 removed outlier: 7.914A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 227 through 229 removed outlier: 7.914A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 79 through 81 removed outlier: 3.575A pdb=" N LEU F 55 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP F 95 " --> pdb=" O LEU F 55 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA F 112 " --> pdb=" O ARG F 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 227 through 229 removed outlier: 6.450A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LEU F 320 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY F 174 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA F 319 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE F 176 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 64 through 66 removed outlier: 4.404A pdb=" N ILE I 49 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS I 100 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 226 through 231 removed outlier: 5.626A pdb=" N VAL I 206 " --> pdb=" O VAL I 228 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER I 230 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU I 208 " --> pdb=" O SER I 230 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET I 205 " --> pdb=" O ILE I 261 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU I 263 " --> pdb=" O MET I 205 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR I 314 " --> pdb=" O VAL I 260 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR I 318 " --> pdb=" O LEU I 264 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU I 342 " --> pdb=" O GLY I 364 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY I 364 " --> pdb=" O GLU I 342 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 118 through 119 removed outlier: 7.843A pdb=" N TYR J 80 " --> pdb=" O LEU J 113 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE J 49 " --> pdb=" O ILE J 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 138 through 139 removed outlier: 4.006A pdb=" N ASN J 306 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 227 through 231 removed outlier: 7.720A pdb=" N VAL J 228 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL J 206 " --> pdb=" O VAL J 228 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER J 230 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU J 208 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL J 260 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE J 316 " --> pdb=" O VAL J 260 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE J 262 " --> pdb=" O ILE J 316 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR J 318 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU J 264 " --> pdb=" O THR J 318 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N LEU J 320 " --> pdb=" O LEU J 264 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY J 174 " --> pdb=" O ALA J 317 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA J 319 " --> pdb=" O GLY J 174 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE J 176 " --> pdb=" O ALA J 319 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 284 through 285 Processing sheet with id=AC9, first strand: chain 'K' and resid 79 through 81 removed outlier: 6.363A pdb=" N THR K 96 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL K 119 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER K 98 " --> pdb=" O ASN K 117 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 138 through 139 removed outlier: 3.615A pdb=" N ASN K 306 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL K 228 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL K 206 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N SER K 230 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU K 208 " --> pdb=" O SER K 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 138 through 139 removed outlier: 3.615A pdb=" N ASN K 306 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY K 174 " --> pdb=" O ALA K 317 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA K 319 " --> pdb=" O GLY K 174 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE K 176 " --> pdb=" O ALA K 319 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET K 341 " --> pdb=" O ARG K 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY K 364 " --> pdb=" O GLU K 342 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 79 through 81 removed outlier: 6.215A pdb=" N THR L 96 " --> pdb=" O VAL L 119 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL L 119 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER L 98 " --> pdb=" O ASN L 117 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ARG L 102 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU L 113 " --> pdb=" O ARG L 102 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 138 through 139 removed outlier: 3.601A pdb=" N ASN L 306 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL L 260 " --> pdb=" O THR L 314 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE L 316 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE L 262 " --> pdb=" O ILE L 316 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR L 318 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU L 264 " --> pdb=" O THR L 318 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N LEU L 320 " --> pdb=" O LEU L 264 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL L 228 " --> pdb=" O LEU L 204 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL L 206 " --> pdb=" O VAL L 228 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER L 230 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU L 208 " --> pdb=" O SER L 230 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 138 through 139 removed outlier: 3.601A pdb=" N ASN L 306 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG L 173 " --> pdb=" O MET L 341 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU L 343 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU L 175 " --> pdb=" O LEU L 343 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N GLU L 342 " --> pdb=" O ASN L 361 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ASN L 361 " --> pdb=" O GLU L 342 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N HIS L 344 " --> pdb=" O ASP L 359 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 64 through 66 removed outlier: 6.551A pdb=" N THR M 96 " --> pdb=" O GLU M 118 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU M 118 " --> pdb=" O THR M 96 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER M 98 " --> pdb=" O VAL M 116 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL M 116 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS M 100 " --> pdb=" O LEU M 114 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 203 through 204 removed outlier: 6.493A pdb=" N VAL M 260 " --> pdb=" O THR M 314 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE M 316 " --> pdb=" O VAL M 260 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE M 262 " --> pdb=" O ILE M 316 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR M 318 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU M 264 " --> pdb=" O THR M 318 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LEU M 320 " --> pdb=" O LEU M 264 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 227 through 229 removed outlier: 6.095A pdb=" N VAL M 206 " --> pdb=" O VAL M 228 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL M 260 " --> pdb=" O THR M 314 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE M 316 " --> pdb=" O VAL M 260 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE M 262 " --> pdb=" O ILE M 316 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR M 318 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU M 264 " --> pdb=" O THR M 318 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LEU M 320 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG M 173 " --> pdb=" O MET M 341 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU M 343 " --> pdb=" O ARG M 173 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU M 175 " --> pdb=" O LEU M 343 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU M 342 " --> pdb=" O GLY M 364 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY M 364 " --> pdb=" O GLU M 342 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 79 through 81 Processing sheet with id=AE1, first strand: chain 'N' and resid 79 through 81 Processing sheet with id=AE2, first strand: chain 'N' and resid 138 through 139 removed outlier: 3.780A pdb=" N ASN N 306 " --> pdb=" O LEU N 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 144 through 145 removed outlier: 4.315A pdb=" N ILE N 168 " --> pdb=" O LEU N 145 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 227 through 229 removed outlier: 7.470A pdb=" N VAL N 228 " --> pdb=" O LEU N 204 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL N 206 " --> pdb=" O VAL N 228 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL N 203 " --> pdb=" O ASP N 259 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU N 263 " --> pdb=" O MET N 205 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL N 260 " --> pdb=" O THR N 314 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE N 316 " --> pdb=" O VAL N 260 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE N 262 " --> pdb=" O ILE N 316 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR N 318 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU N 264 " --> pdb=" O THR N 318 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N LEU N 320 " --> pdb=" O LEU N 264 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU N 175 " --> pdb=" O LEU N 343 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY N 364 " --> pdb=" O GLU N 342 " (cutoff:3.500A) 3199 hydrogen bonds defined for protein. 9279 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: 22.21 Time building geometry restraints manager: 13.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 18954 1.36 - 1.50: 12856 1.50 - 1.65: 23241 1.65 - 1.80: 322 1.80 - 1.95: 166 Bond restraints: 55539 Sorted by residual: bond pdb=" SD MET M 396 " pdb=" CE MET M 396 " ideal model delta sigma weight residual 1.791 1.750 0.041 2.50e-02 1.60e+03 2.66e+00 bond pdb=" CG GLU d 128 " pdb=" CD GLU d 128 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.32e+00 bond pdb=" CG MET B 416 " pdb=" SD MET B 416 " ideal model delta sigma weight residual 1.803 1.768 0.035 2.50e-02 1.60e+03 1.99e+00 bond pdb=" CG GLN a 22 " pdb=" CD GLN a 22 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.89e+00 bond pdb=" C ALA a 101 " pdb=" N PRO a 102 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.87e+00 ... (remaining 55534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 73631 2.10 - 4.20: 1026 4.20 - 6.29: 213 6.29 - 8.39: 37 8.39 - 10.49: 7 Bond angle restraints: 74914 Sorted by residual: angle pdb=" C GLU A 414 " pdb=" N MET A 415 " pdb=" CA MET A 415 " ideal model delta sigma weight residual 122.38 112.87 9.51 1.81e+00 3.05e-01 2.76e+01 angle pdb=" C MET B 415 " pdb=" N MET B 416 " pdb=" CA MET B 416 " ideal model delta sigma weight residual 121.66 113.52 8.14 1.76e+00 3.23e-01 2.14e+01 angle pdb=" N GLU b 128 " pdb=" CA GLU b 128 " pdb=" CB GLU b 128 " ideal model delta sigma weight residual 110.28 117.08 -6.80 1.55e+00 4.16e-01 1.92e+01 angle pdb=" N GLN j 64 " pdb=" CA GLN j 64 " pdb=" CB GLN j 64 " ideal model delta sigma weight residual 110.28 117.03 -6.75 1.55e+00 4.16e-01 1.90e+01 angle pdb=" N GLU d 128 " pdb=" CA GLU d 128 " pdb=" CB GLU d 128 " ideal model delta sigma weight residual 110.28 116.82 -6.54 1.55e+00 4.16e-01 1.78e+01 ... (remaining 74909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 31171 17.95 - 35.89: 2778 35.89 - 53.84: 364 53.84 - 71.78: 79 71.78 - 89.73: 35 Dihedral angle restraints: 34427 sinusoidal: 14467 harmonic: 19960 Sorted by residual: dihedral pdb=" CA LYS d 136 " pdb=" C LYS d 136 " pdb=" N GLY d 137 " pdb=" CA GLY d 137 " ideal model delta harmonic sigma weight residual 180.00 153.02 26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA MET F 415 " pdb=" C MET F 415 " pdb=" N MET F 416 " pdb=" CA MET F 416 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ARG I 28 " pdb=" C ARG I 28 " pdb=" N MET I 29 " pdb=" CA MET I 29 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 34424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 6421 0.046 - 0.091: 1565 0.091 - 0.137: 471 0.137 - 0.183: 29 0.183 - 0.228: 4 Chirality restraints: 8490 Sorted by residual: chirality pdb=" CG LEU M 345 " pdb=" CB LEU M 345 " pdb=" CD1 LEU M 345 " pdb=" CD2 LEU M 345 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU E 26 " pdb=" CB LEU E 26 " pdb=" CD1 LEU E 26 " pdb=" CD2 LEU E 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ARG A 109 " pdb=" N ARG A 109 " pdb=" C ARG A 109 " pdb=" CB ARG A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 8487 not shown) Planarity restraints: 9757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 381 " 0.030 2.00e-02 2.50e+03 2.87e-02 2.05e+01 pdb=" CG TRP A 381 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP A 381 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A 381 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 381 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 381 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 381 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 381 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 381 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP h 133 " -0.019 2.00e-02 2.50e+03 1.79e-02 8.02e+00 pdb=" CG TRP h 133 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP h 133 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP h 133 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP h 133 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP h 133 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP h 133 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP h 133 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP h 133 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP h 133 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG j 23 " -0.227 9.50e-02 1.11e+02 1.02e-01 6.81e+00 pdb=" NE ARG j 23 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG j 23 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG j 23 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG j 23 " -0.012 2.00e-02 2.50e+03 ... (remaining 9754 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 311 2.44 - 3.06: 36391 3.06 - 3.67: 89774 3.67 - 4.29: 123461 4.29 - 4.90: 202394 Nonbonded interactions: 452331 Sorted by model distance: nonbonded pdb=" O3G AGS F 501 " pdb="MG MG F 502 " model vdw 1.825 2.170 nonbonded pdb=" OG1 THR J 185 " pdb="MG MG J 502 " model vdw 2.048 2.170 nonbonded pdb=" OG1 THR D 185 " pdb="MG MG D 502 " model vdw 2.050 2.170 nonbonded pdb=" OG1 THR C 185 " pdb="MG MG C 502 " model vdw 2.055 2.170 nonbonded pdb=" OG1 THR L 185 " pdb="MG MG L 502 " model vdw 2.057 2.170 ... (remaining 452326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = (chain 'B' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = (chain 'D' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = (chain 'E' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = (chain 'F' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = chain 'I' selection = (chain 'J' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = (chain 'K' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = (chain 'L' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = (chain 'M' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) selection = (chain 'N' and (resid 1 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB or name OG )) or resid 501 through 502)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.060 Extract box with map and model: 1.850 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 98.430 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.390 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 : 0.003 0.051 55539 Z= 0.171 Angle : 0.637 10.489 74914 Z= 0.336 Chirality : 0.043 0.228 8490 Planarity : 0.004 0.102 9757 Dihedral : 13.392 89.727 21467 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.10 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 6854 helix: 1.27 (0.09), residues: 3686 sheet: 0.40 (0.20), residues: 686 loop : -0.46 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP A 381 HIS 0.010 0.001 HIS j 78 PHE 0.028 0.001 PHE B 412 TYR 0.020 0.001 TYR f 69 ARG 0.015 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1145 time to evaluate : 4.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8526 (m-10) cc_final: 0.8286 (m-80) REVERT: A 380 MET cc_start: 0.8138 (tpt) cc_final: 0.7630 (tmm) REVERT: B 15 ILE cc_start: 0.9426 (pt) cc_final: 0.9166 (mt) REVERT: B 26 LEU cc_start: 0.8621 (mt) cc_final: 0.8376 (mt) REVERT: B 33 ASP cc_start: 0.8347 (t70) cc_final: 0.7984 (t0) REVERT: B 39 LEU cc_start: 0.8679 (tp) cc_final: 0.8451 (tp) REVERT: C 47 GLU cc_start: 0.8522 (mp0) cc_final: 0.8196 (mp0) REVERT: C 244 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8442 (mm-30) REVERT: C 326 LYS cc_start: 0.8307 (ptmm) cc_final: 0.7673 (ptmm) REVERT: D 29 MET cc_start: 0.8602 (pmm) cc_final: 0.8268 (pmm) REVERT: D 147 MET cc_start: 0.8903 (mmt) cc_final: 0.8511 (mmp) REVERT: D 326 LYS cc_start: 0.8677 (ptpp) cc_final: 0.8422 (pttm) REVERT: E 2 ASN cc_start: 0.8546 (m-40) cc_final: 0.8298 (m-40) REVERT: E 34 ILE cc_start: 0.9404 (mm) cc_final: 0.9155 (mm) REVERT: E 41 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8525 (tm-30) REVERT: E 52 ASP cc_start: 0.8374 (m-30) cc_final: 0.7373 (m-30) REVERT: E 329 GLU cc_start: 0.8308 (tp30) cc_final: 0.7839 (tp30) REVERT: E 342 GLU cc_start: 0.7619 (tt0) cc_final: 0.7342 (tt0) REVERT: E 378 GLN cc_start: 0.8737 (mp10) cc_final: 0.8310 (mp10) REVERT: E 401 ASN cc_start: 0.8748 (m-40) cc_final: 0.8438 (m-40) REVERT: F 329 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8640 (mm-30) REVERT: F 369 GLU cc_start: 0.8739 (pp20) cc_final: 0.8516 (pm20) REVERT: F 405 MET cc_start: 0.9223 (ppp) cc_final: 0.8781 (ppp) REVERT: F 415 MET cc_start: 0.8412 (ppp) cc_final: 0.8137 (ppp) REVERT: I 292 ASN cc_start: 0.7436 (m110) cc_final: 0.7145 (m-40) REVERT: J 8 ASN cc_start: 0.8877 (m-40) cc_final: 0.8635 (m110) REVERT: J 342 GLU cc_start: 0.7248 (pp20) cc_final: 0.6967 (pp20) REVERT: K 57 ILE cc_start: 0.9319 (pt) cc_final: 0.9078 (mm) REVERT: L 215 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8436 (mm-30) REVERT: L 322 ASP cc_start: 0.8849 (m-30) cc_final: 0.8543 (m-30) REVERT: L 326 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8497 (mmmm) REVERT: M 21 MET cc_start: 0.3518 (tmm) cc_final: 0.3115 (ttp) REVERT: M 58 LEU cc_start: 0.8411 (mm) cc_final: 0.8080 (mm) REVERT: M 220 GLN cc_start: 0.8722 (mt0) cc_final: 0.8381 (mp10) REVERT: N 89 PHE cc_start: 0.3991 (t80) cc_final: 0.3779 (t80) REVERT: N 93 THR cc_start: 0.7646 (p) cc_final: 0.7326 (m) REVERT: N 219 MET cc_start: 0.7561 (mmp) cc_final: 0.7005 (mmp) REVERT: N 233 ASP cc_start: 0.8346 (m-30) cc_final: 0.8083 (m-30) REVERT: N 256 HIS cc_start: 0.8299 (m-70) cc_final: 0.8068 (m90) REVERT: N 405 MET cc_start: 0.8746 (ppp) cc_final: 0.8450 (ppp) REVERT: a 21 LEU cc_start: 0.8848 (mt) cc_final: 0.8594 (mt) REVERT: a 69 TYR cc_start: 0.8037 (t80) cc_final: 0.7783 (t80) REVERT: a 83 ASP cc_start: 0.8031 (m-30) cc_final: 0.7596 (m-30) REVERT: a 146 ASP cc_start: 0.8855 (m-30) cc_final: 0.8578 (m-30) REVERT: b 11 ASP cc_start: 0.9093 (m-30) cc_final: 0.8856 (m-30) REVERT: b 116 ASN cc_start: 0.8532 (m110) cc_final: 0.8180 (p0) REVERT: c 83 ASP cc_start: 0.8950 (t0) cc_final: 0.8603 (t0) REVERT: c 109 GLU cc_start: 0.9000 (tp30) cc_final: 0.8759 (tp30) REVERT: c 175 MET cc_start: 0.9127 (pmm) cc_final: 0.8806 (pmm) REVERT: d 168 LYS cc_start: 0.9250 (mmtm) cc_final: 0.9010 (mmtm) REVERT: d 183 GLN cc_start: 0.9281 (tp40) cc_final: 0.8968 (tp40) REVERT: e 120 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8443 (tp40) REVERT: e 124 ASP cc_start: 0.9326 (p0) cc_final: 0.9012 (p0) REVERT: e 183 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8762 (tm-30) REVERT: f 83 ASP cc_start: 0.8715 (m-30) cc_final: 0.8139 (m-30) REVERT: f 87 ASP cc_start: 0.9196 (m-30) cc_final: 0.8992 (m-30) REVERT: f 128 GLU cc_start: 0.9012 (tp30) cc_final: 0.8703 (tp30) REVERT: g 50 GLU cc_start: 0.8551 (pp20) cc_final: 0.8269 (pp20) REVERT: g 141 ASN cc_start: 0.8995 (t0) cc_final: 0.8788 (t0) REVERT: h 49 ASP cc_start: 0.9047 (m-30) cc_final: 0.8767 (m-30) REVERT: h 74 GLU cc_start: 0.8890 (tp30) cc_final: 0.8555 (tp30) REVERT: h 168 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8481 (mptt) REVERT: h 175 MET cc_start: 0.9198 (ptm) cc_final: 0.8984 (ptm) REVERT: i 141 ASN cc_start: 0.8762 (t0) cc_final: 0.8519 (t0) REVERT: j 138 GLU cc_start: 0.7259 (pp20) cc_final: 0.6403 (pm20) REVERT: j 175 MET cc_start: 0.8602 (pmm) cc_final: 0.8173 (pmm) outliers start: 0 outliers final: 0 residues processed: 1145 average time/residue: 0.5533 time to fit residues: 1029.3824 Evaluate side-chains 820 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 820 time to evaluate : 4.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 567 optimal weight: 0.5980 chunk 509 optimal weight: 0.9980 chunk 282 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 chunk 343 optimal weight: 0.0270 chunk 272 optimal weight: 3.9990 chunk 526 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 320 optimal weight: 7.9990 chunk 392 optimal weight: 0.9990 chunk 610 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 239 HIS A 241 GLN A 292 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN I 135 ASN ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 ASN I 193 GLN I 295 HIS ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN J 193 GLN J 239 HIS ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 HIS ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 2 ASN ** L 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 275 ASN ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 ASN M 239 HIS ** M 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN N 140 HIS N 190 ASN N 344 HIS ** N 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 61 GLN ** e 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 174 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55539 Z= 0.193 Angle : 0.658 9.772 74914 Z= 0.342 Chirality : 0.044 0.192 8490 Planarity : 0.004 0.075 9757 Dihedral : 6.462 62.907 7791 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.77 % Favored : 98.22 % Rotamer: Outliers : 1.15 % Allowed : 9.63 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.10), residues: 6854 helix: 1.42 (0.09), residues: 3744 sheet: 0.34 (0.19), residues: 686 loop : -0.53 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP h 133 HIS 0.016 0.001 HIS N 388 PHE 0.026 0.001 PHE M 89 TYR 0.025 0.002 TYR A 360 ARG 0.015 0.001 ARG N 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 939 time to evaluate : 5.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.8563 (m-10) cc_final: 0.8293 (m-80) REVERT: B 33 ASP cc_start: 0.8373 (t70) cc_final: 0.8027 (t0) REVERT: B 39 LEU cc_start: 0.8688 (tp) cc_final: 0.8448 (tp) REVERT: B 56 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7450 (tm-30) REVERT: B 334 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8188 (tm-30) REVERT: B 341 MET cc_start: 0.9010 (tmm) cc_final: 0.8729 (tmm) REVERT: C 218 GLU cc_start: 0.8269 (tp30) cc_final: 0.7749 (tp30) REVERT: C 244 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8412 (mm-30) REVERT: C 326 LYS cc_start: 0.8304 (ptmm) cc_final: 0.7614 (ptmm) REVERT: C 397 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8585 (mt-10) REVERT: D 109 ARG cc_start: 0.8371 (ptt90) cc_final: 0.7959 (ptt90) REVERT: D 147 MET cc_start: 0.8926 (mmt) cc_final: 0.8515 (mmp) REVERT: D 218 GLU cc_start: 0.8208 (tp30) cc_final: 0.7852 (tp30) REVERT: D 322 ASP cc_start: 0.8833 (t0) cc_final: 0.8622 (t0) REVERT: E 2 ASN cc_start: 0.8498 (m-40) cc_final: 0.8143 (m-40) REVERT: E 52 ASP cc_start: 0.7926 (m-30) cc_final: 0.7170 (m-30) REVERT: E 126 ASN cc_start: 0.9052 (m110) cc_final: 0.8804 (m-40) REVERT: E 329 GLU cc_start: 0.8274 (tp30) cc_final: 0.7804 (tp30) REVERT: E 342 GLU cc_start: 0.7746 (tt0) cc_final: 0.7473 (tt0) REVERT: E 378 GLN cc_start: 0.8803 (mp10) cc_final: 0.8250 (mp10) REVERT: E 401 ASN cc_start: 0.8799 (m-40) cc_final: 0.8499 (m-40) REVERT: F 245 MET cc_start: 0.9070 (ppp) cc_final: 0.8843 (ppp) REVERT: F 335 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.7906 (t80) REVERT: F 369 GLU cc_start: 0.8740 (pp20) cc_final: 0.8468 (pm20) REVERT: F 405 MET cc_start: 0.9251 (ppp) cc_final: 0.8809 (ppp) REVERT: F 416 MET cc_start: 0.8231 (mmm) cc_final: 0.7874 (mmm) REVERT: J 8 ASN cc_start: 0.8750 (m-40) cc_final: 0.8484 (m110) REVERT: K 57 ILE cc_start: 0.9485 (pt) cc_final: 0.9101 (mm) REVERT: L 215 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8504 (mm-30) REVERT: L 244 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8299 (mm-30) REVERT: L 322 ASP cc_start: 0.8836 (m-30) cc_final: 0.8557 (m-30) REVERT: L 326 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8479 (mmmm) REVERT: L 342 GLU cc_start: 0.8345 (tt0) cc_final: 0.8142 (tt0) REVERT: L 405 MET cc_start: 0.8607 (ptt) cc_final: 0.7737 (ppp) REVERT: M 58 LEU cc_start: 0.8481 (mm) cc_final: 0.8134 (mm) REVERT: M 220 GLN cc_start: 0.8700 (mt0) cc_final: 0.8323 (mp10) REVERT: M 244 GLU cc_start: 0.8379 (pp20) cc_final: 0.8163 (pp20) REVERT: M 405 MET cc_start: 0.9028 (ppp) cc_final: 0.8686 (ppp) REVERT: N 93 THR cc_start: 0.7627 (p) cc_final: 0.7377 (m) REVERT: N 140 HIS cc_start: 0.6820 (m-70) cc_final: 0.6524 (m-70) REVERT: N 219 MET cc_start: 0.7375 (mmp) cc_final: 0.6872 (mmp) REVERT: N 241 GLN cc_start: 0.9073 (mp10) cc_final: 0.8850 (pm20) REVERT: N 256 HIS cc_start: 0.8316 (m-70) cc_final: 0.8084 (m90) REVERT: N 380 MET cc_start: 0.7856 (ptm) cc_final: 0.7624 (ptm) REVERT: N 405 MET cc_start: 0.8820 (ppp) cc_final: 0.8556 (ppp) REVERT: N 419 SER cc_start: 0.6821 (p) cc_final: 0.6603 (m) REVERT: a 83 ASP cc_start: 0.8067 (m-30) cc_final: 0.7639 (m-30) REVERT: a 146 ASP cc_start: 0.8801 (m-30) cc_final: 0.8533 (m-30) REVERT: c 83 ASP cc_start: 0.8943 (t0) cc_final: 0.8703 (t0) REVERT: d 183 GLN cc_start: 0.9302 (tp40) cc_final: 0.9022 (tp40) REVERT: e 120 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8466 (tp40) REVERT: f 33 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8757 (tm-30) REVERT: f 83 ASP cc_start: 0.8726 (m-30) cc_final: 0.8146 (m-30) REVERT: f 128 GLU cc_start: 0.9029 (tp30) cc_final: 0.8704 (tp30) REVERT: g 138 GLU cc_start: 0.8000 (pt0) cc_final: 0.7569 (pt0) REVERT: g 141 ASN cc_start: 0.9000 (t0) cc_final: 0.8751 (t0) REVERT: h 49 ASP cc_start: 0.9021 (m-30) cc_final: 0.8735 (m-30) REVERT: h 74 GLU cc_start: 0.8891 (tp30) cc_final: 0.8575 (tp30) REVERT: h 146 ASP cc_start: 0.8615 (p0) cc_final: 0.8409 (p0) REVERT: i 141 ASN cc_start: 0.8822 (t0) cc_final: 0.8498 (t0) REVERT: j 17 LYS cc_start: 0.7916 (ptpp) cc_final: 0.7296 (ptpp) REVERT: j 56 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7974 (mm-30) REVERT: j 138 GLU cc_start: 0.7033 (pp20) cc_final: 0.6650 (pm20) REVERT: j 179 ARG cc_start: 0.8473 (tpp-160) cc_final: 0.8098 (tpm170) outliers start: 67 outliers final: 33 residues processed: 972 average time/residue: 0.5365 time to fit residues: 863.7552 Evaluate side-chains 838 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 804 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 390 MET Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 168 LYS Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 175 MET Chi-restraints excluded: chain j residue 116 ASN Chi-restraints excluded: chain j residue 131 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 339 optimal weight: 10.0000 chunk 189 optimal weight: 0.5980 chunk 507 optimal weight: 20.0000 chunk 415 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 611 optimal weight: 2.9990 chunk 660 optimal weight: 7.9990 chunk 544 optimal weight: 0.2980 chunk 606 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 490 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 241 GLN ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN B 239 HIS B 275 ASN C 241 GLN C 295 HIS ** D 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 ASN ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN E 374 GLN F 239 HIS ** F 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 ASN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 275 ASN ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 275 ASN ** K 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 HIS ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 HIS ** M 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN i 145 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 55539 Z= 0.335 Angle : 0.678 14.558 74914 Z= 0.351 Chirality : 0.045 0.202 8490 Planarity : 0.004 0.051 9757 Dihedral : 6.629 63.131 7791 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.74 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 12.38 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.10), residues: 6854 helix: 1.46 (0.08), residues: 3747 sheet: 0.18 (0.20), residues: 682 loop : -0.53 (0.13), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 381 HIS 0.013 0.002 HIS N 388 PHE 0.022 0.002 PHE D 301 TYR 0.023 0.002 TYR a 69 ARG 0.017 0.001 ARG a 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 852 time to evaluate : 5.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ASP cc_start: 0.8403 (t70) cc_final: 0.7903 (t70) REVERT: B 39 LEU cc_start: 0.8719 (tp) cc_final: 0.8468 (tp) REVERT: B 219 MET cc_start: 0.9271 (tpt) cc_final: 0.9049 (tpt) REVERT: B 329 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: B 341 MET cc_start: 0.9010 (tmm) cc_final: 0.8763 (tmm) REVERT: C 218 GLU cc_start: 0.8434 (tp30) cc_final: 0.7975 (tp30) REVERT: C 244 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8424 (mm-30) REVERT: C 326 LYS cc_start: 0.8477 (ptmm) cc_final: 0.7761 (ptmm) REVERT: C 342 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 405 MET cc_start: 0.8939 (ppp) cc_final: 0.8675 (ppp) REVERT: C 415 MET cc_start: 0.8930 (ttp) cc_final: 0.8720 (ttt) REVERT: D 29 MET cc_start: 0.8630 (pmm) cc_final: 0.8285 (pmm) REVERT: D 109 ARG cc_start: 0.8410 (ptt90) cc_final: 0.8045 (ptt90) REVERT: D 218 GLU cc_start: 0.8448 (tp30) cc_final: 0.8058 (tp30) REVERT: D 322 ASP cc_start: 0.8867 (t0) cc_final: 0.8546 (t0) REVERT: E 87 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8719 (ttp80) REVERT: E 126 ASN cc_start: 0.9074 (m110) cc_final: 0.8823 (m-40) REVERT: E 329 GLU cc_start: 0.8359 (tp30) cc_final: 0.7874 (tp30) REVERT: E 401 ASN cc_start: 0.8843 (m-40) cc_final: 0.8578 (m-40) REVERT: F 241 GLN cc_start: 0.8925 (pt0) cc_final: 0.8579 (mp10) REVERT: F 245 MET cc_start: 0.9055 (ppp) cc_final: 0.8815 (ppp) REVERT: F 369 GLU cc_start: 0.8855 (pp20) cc_final: 0.8568 (pm20) REVERT: F 405 MET cc_start: 0.9254 (ppp) cc_final: 0.8764 (ppp) REVERT: F 415 MET cc_start: 0.8244 (ppp) cc_final: 0.7722 (ppp) REVERT: I 147 MET cc_start: 0.6712 (mmt) cc_final: 0.6474 (tpp) REVERT: I 219 MET cc_start: 0.7981 (mmp) cc_final: 0.7665 (mmp) REVERT: I 416 MET cc_start: 0.3812 (ptt) cc_final: 0.3414 (ptt) REVERT: J 8 ASN cc_start: 0.8655 (m-40) cc_final: 0.8373 (m110) REVERT: J 109 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8452 (mtm110) REVERT: J 110 TYR cc_start: 0.8674 (m-10) cc_final: 0.8307 (m-10) REVERT: K 1 MET cc_start: 0.7317 (tpt) cc_final: 0.7054 (tpp) REVERT: K 30 ARG cc_start: 0.7426 (mmm160) cc_final: 0.7190 (tpp80) REVERT: K 57 ILE cc_start: 0.9538 (pt) cc_final: 0.9098 (mm) REVERT: L 215 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8638 (mm-30) REVERT: L 220 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: L 322 ASP cc_start: 0.8890 (m-30) cc_final: 0.8605 (m-30) REVERT: L 326 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8628 (mmmm) REVERT: L 405 MET cc_start: 0.8812 (ptt) cc_final: 0.7952 (ppp) REVERT: M 58 LEU cc_start: 0.8547 (mm) cc_final: 0.8186 (mm) REVERT: M 193 GLN cc_start: 0.8742 (tt0) cc_final: 0.8451 (tt0) REVERT: M 220 GLN cc_start: 0.8776 (mt0) cc_final: 0.8376 (mp10) REVERT: N 219 MET cc_start: 0.7449 (mmp) cc_final: 0.6898 (mmp) REVERT: N 241 GLN cc_start: 0.9060 (mp10) cc_final: 0.8827 (pm20) REVERT: N 342 GLU cc_start: 0.7374 (pp20) cc_final: 0.7094 (tm-30) REVERT: N 375 GLU cc_start: 0.9135 (mp0) cc_final: 0.8895 (mp0) REVERT: N 388 HIS cc_start: 0.7134 (m-70) cc_final: 0.6647 (m-70) REVERT: N 405 MET cc_start: 0.8789 (ppp) cc_final: 0.8545 (ppp) REVERT: a 22 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8601 (pm20) REVERT: a 53 ASN cc_start: 0.8940 (m-40) cc_final: 0.8622 (t0) REVERT: a 69 TYR cc_start: 0.7885 (t80) cc_final: 0.7656 (t80) REVERT: a 83 ASP cc_start: 0.8049 (m-30) cc_final: 0.7559 (m-30) REVERT: a 146 ASP cc_start: 0.8882 (m-30) cc_final: 0.8616 (m-30) REVERT: b 83 ASP cc_start: 0.8696 (t0) cc_final: 0.8442 (t0) REVERT: b 116 ASN cc_start: 0.8736 (m110) cc_final: 0.8290 (p0) REVERT: c 83 ASP cc_start: 0.8947 (t0) cc_final: 0.8713 (t0) REVERT: c 141 ASN cc_start: 0.9216 (t0) cc_final: 0.9002 (t0) REVERT: d 56 GLU cc_start: 0.8395 (tt0) cc_final: 0.8194 (tt0) REVERT: d 124 ASP cc_start: 0.9331 (p0) cc_final: 0.9094 (p0) REVERT: d 183 GLN cc_start: 0.9349 (tp40) cc_final: 0.9040 (tp40) REVERT: e 120 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8541 (tp40) REVERT: e 183 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8755 (tm-30) REVERT: f 33 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8884 (tm-30) REVERT: f 83 ASP cc_start: 0.8732 (m-30) cc_final: 0.8148 (m-30) REVERT: g 50 GLU cc_start: 0.8774 (pp20) cc_final: 0.8379 (pp20) REVERT: g 89 MET cc_start: 0.8616 (tpp) cc_final: 0.8345 (mmm) REVERT: g 141 ASN cc_start: 0.9104 (t0) cc_final: 0.8877 (t0) REVERT: h 49 ASP cc_start: 0.9066 (m-30) cc_final: 0.8763 (m-30) REVERT: h 50 GLU cc_start: 0.8905 (pp20) cc_final: 0.8618 (pp20) REVERT: h 71 ARG cc_start: 0.8731 (mpp80) cc_final: 0.8058 (mtm-85) REVERT: h 74 GLU cc_start: 0.8954 (tp30) cc_final: 0.8683 (tp30) REVERT: i 141 ASN cc_start: 0.8796 (t0) cc_final: 0.8423 (t0) REVERT: i 168 LYS cc_start: 0.8944 (mmpt) cc_final: 0.8627 (mmmt) REVERT: j 56 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7987 (mm-30) REVERT: j 138 GLU cc_start: 0.7857 (pp20) cc_final: 0.6968 (pm20) REVERT: j 153 ILE cc_start: 0.8071 (mm) cc_final: 0.7842 (tp) REVERT: j 175 MET cc_start: 0.8492 (pmm) cc_final: 0.8228 (pmm) outliers start: 116 outliers final: 71 residues processed: 909 average time/residue: 0.5277 time to fit residues: 797.4836 Evaluate side-chains 844 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 770 time to evaluate : 5.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain I residue 388 HIS Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 390 MET Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 318 THR Chi-restraints excluded: chain M residue 411 ASP Chi-restraints excluded: chain N residue 372 THR Chi-restraints excluded: chain N residue 378 GLN Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain a residue 22 GLN Chi-restraints excluded: chain a residue 59 LYS Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 148 ASP Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain f residue 159 VAL Chi-restraints excluded: chain f residue 168 LYS Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 128 GLU Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 119 ILE Chi-restraints excluded: chain h residue 138 GLU Chi-restraints excluded: chain i residue 12 THR Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 175 MET Chi-restraints excluded: chain j residue 116 ASN Chi-restraints excluded: chain j residue 117 CYS Chi-restraints excluded: chain j residue 131 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 604 optimal weight: 3.9990 chunk 459 optimal weight: 9.9990 chunk 317 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 291 optimal weight: 10.0000 chunk 410 optimal weight: 30.0000 chunk 613 optimal weight: 9.9990 chunk 649 optimal weight: 0.0270 chunk 320 optimal weight: 1.9990 chunk 581 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 292 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS D 344 HIS ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 GLN ** K 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 HIS N 120 ASN N 140 HIS a 15 ASN ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 ASN j 64 GLN j 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 55539 Z= 0.221 Angle : 0.640 12.754 74914 Z= 0.330 Chirality : 0.043 0.183 8490 Planarity : 0.004 0.052 9757 Dihedral : 6.474 62.387 7791 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.84 % Favored : 98.15 % Rotamer: Outliers : 2.19 % Allowed : 13.99 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.10), residues: 6854 helix: 1.49 (0.08), residues: 3755 sheet: 0.15 (0.20), residues: 680 loop : -0.50 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP j 133 HIS 0.010 0.001 HIS a 78 PHE 0.015 0.001 PHE N 355 TYR 0.027 0.002 TYR j 69 ARG 0.008 0.000 ARG J 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 859 time to evaluate : 5.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7716 (ttt) cc_final: 0.7378 (tmm) REVERT: A 388 HIS cc_start: 0.7784 (m-70) cc_final: 0.7412 (m-70) REVERT: B 39 LEU cc_start: 0.8762 (tp) cc_final: 0.8488 (tp) REVERT: B 56 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7772 (tm-30) REVERT: B 326 LYS cc_start: 0.8893 (ptpp) cc_final: 0.8540 (ptmm) REVERT: B 329 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8475 (pm20) REVERT: B 341 MET cc_start: 0.9021 (tmm) cc_final: 0.8712 (tmm) REVERT: B 378 GLN cc_start: 0.9233 (mp10) cc_final: 0.8985 (mp-120) REVERT: C 39 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8657 (tp) REVERT: C 218 GLU cc_start: 0.8428 (tp30) cc_final: 0.7942 (tp30) REVERT: C 234 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8670 (mt-10) REVERT: C 326 LYS cc_start: 0.8425 (ptmm) cc_final: 0.8017 (tttp) REVERT: C 342 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 405 MET cc_start: 0.8932 (ppp) cc_final: 0.8692 (ppp) REVERT: D 29 MET cc_start: 0.8594 (pmm) cc_final: 0.8183 (pmm) REVERT: D 109 ARG cc_start: 0.8428 (ptt90) cc_final: 0.8094 (ptt90) REVERT: D 218 GLU cc_start: 0.8483 (tp30) cc_final: 0.8106 (tp30) REVERT: D 322 ASP cc_start: 0.8836 (t0) cc_final: 0.8445 (t0) REVERT: E 52 ASP cc_start: 0.7592 (m-30) cc_final: 0.7317 (m-30) REVERT: E 87 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8693 (ttp80) REVERT: E 220 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7908 (mt0) REVERT: E 329 GLU cc_start: 0.8315 (tp30) cc_final: 0.7847 (tp30) REVERT: E 401 ASN cc_start: 0.8848 (m-40) cc_final: 0.8559 (m-40) REVERT: F 245 MET cc_start: 0.8995 (ppp) cc_final: 0.8718 (ppp) REVERT: F 369 GLU cc_start: 0.8859 (pp20) cc_final: 0.8538 (pm20) REVERT: F 405 MET cc_start: 0.9236 (ppp) cc_final: 0.8789 (ppp) REVERT: F 415 MET cc_start: 0.8268 (ppp) cc_final: 0.7706 (ppp) REVERT: F 416 MET cc_start: 0.8247 (mmm) cc_final: 0.7950 (mmm) REVERT: I 416 MET cc_start: 0.3694 (ptt) cc_final: 0.2926 (ptt) REVERT: J 8 ASN cc_start: 0.8631 (m-40) cc_final: 0.8405 (m-40) REVERT: J 109 ARG cc_start: 0.8778 (mtm-85) cc_final: 0.8399 (mtm110) REVERT: J 110 TYR cc_start: 0.8633 (m-10) cc_final: 0.8308 (m-10) REVERT: J 415 MET cc_start: 0.8803 (tmm) cc_final: 0.8485 (tpt) REVERT: K 1 MET cc_start: 0.7357 (tpt) cc_final: 0.7037 (tpp) REVERT: K 30 ARG cc_start: 0.7456 (mmm160) cc_final: 0.7208 (tpp80) REVERT: K 57 ILE cc_start: 0.9536 (pt) cc_final: 0.9149 (mm) REVERT: K 134 GLU cc_start: 0.9049 (pm20) cc_final: 0.8827 (pm20) REVERT: L 1 MET cc_start: 0.8667 (mmm) cc_final: 0.8106 (ptt) REVERT: L 215 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8659 (mm-30) REVERT: L 322 ASP cc_start: 0.8871 (m-30) cc_final: 0.8580 (m-30) REVERT: L 326 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8631 (mmmm) REVERT: L 405 MET cc_start: 0.8825 (ptt) cc_final: 0.7923 (ppp) REVERT: M 58 LEU cc_start: 0.8575 (mm) cc_final: 0.8212 (mm) REVERT: M 193 GLN cc_start: 0.8742 (tt0) cc_final: 0.8427 (tt0) REVERT: M 215 GLU cc_start: 0.8855 (mm-30) cc_final: 0.7875 (mt-10) REVERT: N 219 MET cc_start: 0.7489 (mmp) cc_final: 0.7003 (mmp) REVERT: N 241 GLN cc_start: 0.9020 (mp10) cc_final: 0.8797 (pt0) REVERT: N 353 ARG cc_start: 0.5636 (mmp-170) cc_final: 0.5313 (mmp80) REVERT: N 374 GLN cc_start: 0.8982 (mp10) cc_final: 0.8756 (mp10) REVERT: N 375 GLU cc_start: 0.9104 (mp0) cc_final: 0.8689 (mp0) REVERT: N 388 HIS cc_start: 0.7129 (m-70) cc_final: 0.6588 (m-70) REVERT: N 405 MET cc_start: 0.8787 (ppp) cc_final: 0.8518 (ppp) REVERT: a 22 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8552 (pm20) REVERT: a 53 ASN cc_start: 0.8890 (m-40) cc_final: 0.8637 (t0) REVERT: a 69 TYR cc_start: 0.7878 (t80) cc_final: 0.7589 (t80) REVERT: a 83 ASP cc_start: 0.8107 (m-30) cc_final: 0.7667 (m-30) REVERT: a 146 ASP cc_start: 0.8919 (m-30) cc_final: 0.8659 (m-30) REVERT: b 83 ASP cc_start: 0.8731 (t0) cc_final: 0.8477 (t0) REVERT: b 116 ASN cc_start: 0.8780 (m110) cc_final: 0.8330 (p0) REVERT: b 128 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9116 (mm-30) REVERT: c 141 ASN cc_start: 0.9248 (t0) cc_final: 0.8975 (t0) REVERT: d 104 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8677 (mm) REVERT: d 124 ASP cc_start: 0.9362 (p0) cc_final: 0.9154 (p0) REVERT: d 183 GLN cc_start: 0.9312 (tp40) cc_final: 0.9022 (tp40) REVERT: e 120 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8540 (tp40) REVERT: e 162 VAL cc_start: 0.9262 (m) cc_final: 0.8838 (m) REVERT: e 168 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8549 (mmmt) REVERT: e 183 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8773 (tm-30) REVERT: f 83 ASP cc_start: 0.8743 (m-30) cc_final: 0.8155 (m-30) REVERT: g 89 MET cc_start: 0.8730 (tpp) cc_final: 0.8448 (mmm) REVERT: h 49 ASP cc_start: 0.9045 (m-30) cc_final: 0.8725 (m-30) REVERT: h 50 GLU cc_start: 0.8917 (pp20) cc_final: 0.8610 (pp20) REVERT: h 71 ARG cc_start: 0.8739 (mpp80) cc_final: 0.8069 (mtm-85) REVERT: h 74 GLU cc_start: 0.8938 (tp30) cc_final: 0.8644 (tp30) REVERT: i 141 ASN cc_start: 0.8740 (t0) cc_final: 0.8345 (t0) REVERT: i 168 LYS cc_start: 0.8928 (mmpt) cc_final: 0.8612 (mmmt) REVERT: j 56 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7846 (mt-10) REVERT: j 138 GLU cc_start: 0.7698 (pp20) cc_final: 0.7005 (pm20) REVERT: j 175 MET cc_start: 0.8548 (pmm) cc_final: 0.8105 (pmm) REVERT: j 179 ARG cc_start: 0.8559 (tpp-160) cc_final: 0.8137 (tpm170) outliers start: 128 outliers final: 80 residues processed: 930 average time/residue: 0.5164 time to fit residues: 805.5835 Evaluate side-chains 854 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 768 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 388 HIS Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 326 LYS Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 244 GLU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 372 THR Chi-restraints excluded: chain N residue 378 GLN Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain a residue 22 GLN Chi-restraints excluded: chain a residue 59 LYS Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 170 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 83 ASP Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain e residue 134 LEU Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 168 LYS Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain g residue 175 MET Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 78 HIS Chi-restraints excluded: chain i residue 175 MET Chi-restraints excluded: chain j residue 116 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 540 optimal weight: 0.9980 chunk 368 optimal weight: 2.9990 chunk 9 optimal weight: 0.0020 chunk 483 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 554 optimal weight: 2.9990 chunk 448 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 331 optimal weight: 8.9990 chunk 583 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN L 193 GLN ** M 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55539 Z= 0.202 Angle : 0.631 12.479 74914 Z= 0.325 Chirality : 0.043 0.193 8490 Planarity : 0.004 0.050 9757 Dihedral : 6.363 61.832 7791 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.72 % Favored : 98.26 % Rotamer: Outliers : 2.33 % Allowed : 14.70 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.10), residues: 6854 helix: 1.55 (0.08), residues: 3773 sheet: 0.17 (0.20), residues: 680 loop : -0.41 (0.13), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP g 133 HIS 0.008 0.001 HIS N 388 PHE 0.014 0.001 PHE B 412 TYR 0.021 0.002 TYR j 69 ARG 0.009 0.000 ARG f 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 846 time to evaluate : 5.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7903 (ttt) cc_final: 0.7480 (tmm) REVERT: A 244 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 387 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8160 (tt) REVERT: A 388 HIS cc_start: 0.7791 (m-70) cc_final: 0.7462 (m-70) REVERT: B 39 LEU cc_start: 0.8728 (tp) cc_final: 0.8439 (tp) REVERT: B 219 MET cc_start: 0.9250 (tpt) cc_final: 0.9038 (tpt) REVERT: B 326 LYS cc_start: 0.8890 (ptpp) cc_final: 0.8554 (ptmm) REVERT: B 329 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: B 341 MET cc_start: 0.9009 (tmm) cc_final: 0.8687 (tmm) REVERT: B 378 GLN cc_start: 0.9234 (mp10) cc_final: 0.8973 (mp10) REVERT: C 39 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8649 (tp) REVERT: C 218 GLU cc_start: 0.8425 (tp30) cc_final: 0.7929 (tp30) REVERT: C 234 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8635 (mt-10) REVERT: C 326 LYS cc_start: 0.8539 (ptmm) cc_final: 0.8177 (tttp) REVERT: D 29 MET cc_start: 0.8575 (pmm) cc_final: 0.8291 (pmm) REVERT: D 109 ARG cc_start: 0.8410 (ptt90) cc_final: 0.8090 (ptt90) REVERT: D 218 GLU cc_start: 0.8538 (tp30) cc_final: 0.8142 (tp30) REVERT: D 322 ASP cc_start: 0.8831 (t0) cc_final: 0.8424 (t0) REVERT: E 29 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7184 (ptp) REVERT: E 87 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8701 (ttp80) REVERT: E 220 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: E 308 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8586 (mt-10) REVERT: E 329 GLU cc_start: 0.8296 (tp30) cc_final: 0.7828 (tp30) REVERT: E 401 ASN cc_start: 0.8838 (m-40) cc_final: 0.8550 (m-40) REVERT: F 29 MET cc_start: 0.4159 (ptt) cc_final: 0.3584 (ttp) REVERT: F 245 MET cc_start: 0.8957 (ppp) cc_final: 0.8715 (ppp) REVERT: F 342 GLU cc_start: 0.7655 (pp20) cc_final: 0.7191 (pp20) REVERT: F 369 GLU cc_start: 0.8850 (pp20) cc_final: 0.8498 (pm20) REVERT: F 405 MET cc_start: 0.9243 (ppp) cc_final: 0.8836 (ppp) REVERT: I 416 MET cc_start: 0.3639 (ptt) cc_final: 0.3057 (ptt) REVERT: J 8 ASN cc_start: 0.8646 (m-40) cc_final: 0.8411 (m-40) REVERT: J 109 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8370 (mtm110) REVERT: J 110 TYR cc_start: 0.8626 (m-10) cc_final: 0.8333 (m-10) REVERT: J 136 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8485 (mp) REVERT: J 415 MET cc_start: 0.8826 (tmm) cc_final: 0.8476 (tpt) REVERT: K 1 MET cc_start: 0.7472 (tpt) cc_final: 0.7148 (tpp) REVERT: K 30 ARG cc_start: 0.7468 (mmm160) cc_final: 0.7265 (tpp80) REVERT: K 56 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8157 (tm-30) REVERT: K 57 ILE cc_start: 0.9532 (pt) cc_final: 0.9189 (mm) REVERT: L 88 ARG cc_start: 0.8567 (ptt-90) cc_final: 0.8347 (ptt-90) REVERT: L 215 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8656 (mm-30) REVERT: L 220 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: L 322 ASP cc_start: 0.8861 (m-30) cc_final: 0.8579 (m-30) REVERT: L 326 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8634 (mmmm) REVERT: L 405 MET cc_start: 0.8852 (ptt) cc_final: 0.7943 (ppp) REVERT: M 58 LEU cc_start: 0.8557 (mm) cc_final: 0.8171 (mm) REVERT: M 193 GLN cc_start: 0.8748 (tt0) cc_final: 0.8446 (tt0) REVERT: N 147 MET cc_start: 0.6925 (mmp) cc_final: 0.6700 (tpp) REVERT: N 219 MET cc_start: 0.7510 (mmp) cc_final: 0.7050 (mmp) REVERT: N 241 GLN cc_start: 0.9032 (mp10) cc_final: 0.8810 (pt0) REVERT: N 342 GLU cc_start: 0.7268 (pp20) cc_final: 0.7011 (tm-30) REVERT: N 375 GLU cc_start: 0.9106 (mp0) cc_final: 0.8845 (mp0) REVERT: N 388 HIS cc_start: 0.7190 (m-70) cc_final: 0.6675 (m-70) REVERT: N 405 MET cc_start: 0.8867 (ppp) cc_final: 0.8544 (ppp) REVERT: a 22 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: a 53 ASN cc_start: 0.8920 (m-40) cc_final: 0.8677 (t0) REVERT: a 83 ASP cc_start: 0.8135 (m-30) cc_final: 0.7709 (m-30) REVERT: a 146 ASP cc_start: 0.8925 (m-30) cc_final: 0.8651 (m-30) REVERT: b 83 ASP cc_start: 0.8765 (t0) cc_final: 0.8504 (t0) REVERT: b 128 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9106 (mm-30) REVERT: b 142 TYR cc_start: 0.7732 (m-80) cc_final: 0.7523 (m-80) REVERT: c 141 ASN cc_start: 0.9275 (t0) cc_final: 0.9028 (t0) REVERT: d 104 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8651 (mm) REVERT: d 183 GLN cc_start: 0.9304 (tp40) cc_final: 0.9017 (tp40) REVERT: e 120 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8506 (tp40) REVERT: e 168 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8538 (mmmt) REVERT: e 183 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8782 (tm-30) REVERT: f 83 ASP cc_start: 0.8745 (m-30) cc_final: 0.8155 (m-30) REVERT: g 89 MET cc_start: 0.8819 (tpp) cc_final: 0.8379 (tpp) REVERT: g 142 TYR cc_start: 0.8377 (m-80) cc_final: 0.7976 (m-80) REVERT: h 49 ASP cc_start: 0.9042 (m-30) cc_final: 0.8721 (m-30) REVERT: h 50 GLU cc_start: 0.8960 (pp20) cc_final: 0.8541 (pp20) REVERT: h 71 ARG cc_start: 0.8741 (mpp80) cc_final: 0.8076 (mtm-85) REVERT: h 74 GLU cc_start: 0.8930 (tp30) cc_final: 0.8628 (tp30) REVERT: i 141 ASN cc_start: 0.8721 (t0) cc_final: 0.8323 (t0) REVERT: i 168 LYS cc_start: 0.8925 (mmpt) cc_final: 0.8621 (mmmt) REVERT: j 56 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7973 (mm-30) REVERT: j 138 GLU cc_start: 0.8000 (pp20) cc_final: 0.7173 (pm20) REVERT: j 179 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8073 (tpm170) outliers start: 136 outliers final: 84 residues processed: 926 average time/residue: 0.5119 time to fit residues: 791.8011 Evaluate side-chains 869 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 775 time to evaluate : 4.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 388 HIS Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 393 ILE Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 326 LYS Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 372 THR Chi-restraints excluded: chain N residue 378 GLN Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain N residue 398 PHE Chi-restraints excluded: chain a residue 22 GLN Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 83 ASP Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain e residue 134 LEU Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 168 LYS Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain h residue 119 ILE Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 78 HIS Chi-restraints excluded: chain i residue 175 MET Chi-restraints excluded: chain j residue 116 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 218 optimal weight: 6.9990 chunk 584 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 381 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 650 optimal weight: 2.9990 chunk 539 optimal weight: 8.9990 chunk 301 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 215 optimal weight: 0.0870 chunk 341 optimal weight: 3.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 55539 Z= 0.247 Angle : 0.660 12.660 74914 Z= 0.339 Chirality : 0.044 0.254 8490 Planarity : 0.004 0.059 9757 Dihedral : 6.404 61.632 7791 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.88 % Favored : 98.10 % Rotamer: Outliers : 2.38 % Allowed : 15.95 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.10), residues: 6854 helix: 1.55 (0.08), residues: 3791 sheet: 0.13 (0.19), residues: 699 loop : -0.40 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP i 133 HIS 0.008 0.001 HIS e 73 PHE 0.014 0.001 PHE D 301 TYR 0.020 0.002 TYR F 274 ARG 0.014 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 812 time to evaluate : 5.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 388 HIS cc_start: 0.7837 (m-70) cc_final: 0.7514 (m-70) REVERT: B 326 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8552 (ptmm) REVERT: B 329 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: B 341 MET cc_start: 0.9035 (tmm) cc_final: 0.8713 (tmm) REVERT: B 378 GLN cc_start: 0.9232 (mp10) cc_final: 0.8958 (mp10) REVERT: C 39 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8709 (tp) REVERT: C 218 GLU cc_start: 0.8451 (tp30) cc_final: 0.7984 (tp30) REVERT: C 234 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8663 (mt-10) REVERT: C 326 LYS cc_start: 0.8602 (ptmm) cc_final: 0.8200 (pttp) REVERT: C 392 GLU cc_start: 0.8166 (pm20) cc_final: 0.7551 (pt0) REVERT: D 29 MET cc_start: 0.8537 (pmm) cc_final: 0.8218 (pmm) REVERT: D 109 ARG cc_start: 0.8431 (ptt90) cc_final: 0.8125 (ptt90) REVERT: D 218 GLU cc_start: 0.8578 (tp30) cc_final: 0.8109 (tp30) REVERT: D 322 ASP cc_start: 0.8838 (t0) cc_final: 0.8418 (t0) REVERT: D 326 LYS cc_start: 0.8742 (tppt) cc_final: 0.8393 (tppp) REVERT: E 29 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7240 (ptp) REVERT: E 87 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8719 (ttp80) REVERT: E 220 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: E 329 GLU cc_start: 0.8320 (tp30) cc_final: 0.7845 (tp30) REVERT: E 401 ASN cc_start: 0.8819 (m-40) cc_final: 0.8526 (m-40) REVERT: F 29 MET cc_start: 0.4183 (ptt) cc_final: 0.3486 (ttp) REVERT: F 245 MET cc_start: 0.8913 (ppp) cc_final: 0.8680 (ppp) REVERT: F 334 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8789 (tm-30) REVERT: F 335 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8327 (t80) REVERT: F 342 GLU cc_start: 0.7656 (pp20) cc_final: 0.7182 (pp20) REVERT: F 369 GLU cc_start: 0.8878 (pp20) cc_final: 0.8541 (pm20) REVERT: F 405 MET cc_start: 0.9271 (ppp) cc_final: 0.8976 (ppp) REVERT: F 415 MET cc_start: 0.8248 (ppp) cc_final: 0.7720 (ppp) REVERT: I 30 ARG cc_start: 0.6852 (tpm170) cc_final: 0.6484 (tpp80) REVERT: I 327 MET cc_start: 0.7650 (ptm) cc_final: 0.7414 (ptm) REVERT: I 406 THR cc_start: 0.6699 (OUTLIER) cc_final: 0.6404 (m) REVERT: I 416 MET cc_start: 0.3723 (ptt) cc_final: 0.3407 (ptt) REVERT: J 8 ASN cc_start: 0.8635 (m-40) cc_final: 0.8394 (m-40) REVERT: J 109 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8371 (mtm110) REVERT: J 110 TYR cc_start: 0.8622 (m-10) cc_final: 0.8345 (m-10) REVERT: J 136 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8560 (mp) REVERT: J 344 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8537 (m170) REVERT: J 374 GLN cc_start: 0.8311 (tp40) cc_final: 0.7860 (tp40) REVERT: J 415 MET cc_start: 0.8861 (tmm) cc_final: 0.8493 (tpt) REVERT: K 1 MET cc_start: 0.7513 (tpt) cc_final: 0.7257 (tpp) REVERT: K 56 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8111 (tm-30) REVERT: K 57 ILE cc_start: 0.9541 (pt) cc_final: 0.9235 (mm) REVERT: L 85 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: L 88 ARG cc_start: 0.8606 (ptt-90) cc_final: 0.8321 (ptt90) REVERT: L 215 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8653 (mm-30) REVERT: L 220 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: L 322 ASP cc_start: 0.8877 (m-30) cc_final: 0.8596 (m-30) REVERT: L 326 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8673 (mmmm) REVERT: M 58 LEU cc_start: 0.8579 (mm) cc_final: 0.8187 (mm) REVERT: M 72 TYR cc_start: 0.6993 (m-80) cc_final: 0.6738 (m-80) REVERT: M 353 ARG cc_start: 0.8307 (mpp80) cc_final: 0.8097 (mpp80) REVERT: N 241 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8812 (pt0) REVERT: N 375 GLU cc_start: 0.9113 (mp0) cc_final: 0.8759 (mp0) REVERT: N 388 HIS cc_start: 0.7291 (m-70) cc_final: 0.6751 (m-70) REVERT: N 405 MET cc_start: 0.8829 (ppp) cc_final: 0.8616 (ppp) REVERT: a 53 ASN cc_start: 0.8947 (m-40) cc_final: 0.8729 (t0) REVERT: a 83 ASP cc_start: 0.8168 (m-30) cc_final: 0.7745 (m-30) REVERT: a 146 ASP cc_start: 0.8994 (m-30) cc_final: 0.8736 (m-30) REVERT: a 164 ASP cc_start: 0.8249 (m-30) cc_final: 0.7821 (m-30) REVERT: b 83 ASP cc_start: 0.8783 (t0) cc_final: 0.8514 (t0) REVERT: b 128 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9122 (mm-30) REVERT: c 141 ASN cc_start: 0.9265 (t0) cc_final: 0.8996 (t0) REVERT: d 104 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8650 (mm) REVERT: d 168 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8670 (mmmt) REVERT: d 183 GLN cc_start: 0.9306 (tp40) cc_final: 0.9023 (tp40) REVERT: e 120 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8542 (tp40) REVERT: e 168 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8565 (mmmt) REVERT: e 183 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8798 (tm-30) REVERT: f 83 ASP cc_start: 0.8767 (m-30) cc_final: 0.8172 (m-30) REVERT: g 142 TYR cc_start: 0.8381 (m-80) cc_final: 0.7994 (m-80) REVERT: h 49 ASP cc_start: 0.9049 (m-30) cc_final: 0.8714 (m-30) REVERT: h 50 GLU cc_start: 0.8961 (pp20) cc_final: 0.8602 (pp20) REVERT: h 71 ARG cc_start: 0.8752 (mpp80) cc_final: 0.8124 (mtm-85) REVERT: h 74 GLU cc_start: 0.8958 (tp30) cc_final: 0.8653 (tp30) REVERT: i 141 ASN cc_start: 0.8736 (t0) cc_final: 0.8346 (t0) REVERT: i 168 LYS cc_start: 0.8915 (mmpt) cc_final: 0.8640 (mmmt) REVERT: j 17 LYS cc_start: 0.7861 (ptpp) cc_final: 0.7161 (ptpt) REVERT: j 56 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8021 (mt-10) REVERT: j 138 GLU cc_start: 0.7968 (pp20) cc_final: 0.7156 (pm20) REVERT: j 153 ILE cc_start: 0.7989 (mm) cc_final: 0.7616 (tp) REVERT: j 175 MET cc_start: 0.8452 (pmm) cc_final: 0.8240 (pmm) REVERT: j 179 ARG cc_start: 0.8553 (tpp-160) cc_final: 0.8073 (tpm170) outliers start: 139 outliers final: 96 residues processed: 901 average time/residue: 0.5107 time to fit residues: 770.8721 Evaluate side-chains 877 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 768 time to evaluate : 5.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 388 HIS Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain I residue 388 HIS Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 344 HIS Chi-restraints excluded: chain J residue 393 ILE Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 326 LYS Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 411 ASP Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 372 THR Chi-restraints excluded: chain N residue 378 GLN Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 59 LYS Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 168 LYS Chi-restraints excluded: chain a residue 170 THR Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 83 ASP Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain e residue 17 LYS Chi-restraints excluded: chain e residue 134 LEU Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 168 LYS Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain h residue 119 ILE Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 175 MET Chi-restraints excluded: chain j residue 86 ASN Chi-restraints excluded: chain j residue 116 ASN Chi-restraints excluded: chain j residue 117 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 626 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 370 optimal weight: 5.9990 chunk 474 optimal weight: 7.9990 chunk 367 optimal weight: 3.9990 chunk 547 optimal weight: 4.9990 chunk 363 optimal weight: 1.9990 chunk 647 optimal weight: 0.9990 chunk 405 optimal weight: 0.1980 chunk 394 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS C 85 GLN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN ** a 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 ASN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 55539 Z= 0.197 Angle : 0.668 15.873 74914 Z= 0.340 Chirality : 0.044 0.226 8490 Planarity : 0.004 0.051 9757 Dihedral : 6.314 61.027 7791 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.72 % Favored : 98.26 % Rotamer: Outliers : 2.40 % Allowed : 16.74 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.10), residues: 6854 helix: 1.57 (0.08), residues: 3791 sheet: 0.17 (0.20), residues: 706 loop : -0.38 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP i 133 HIS 0.012 0.001 HIS N 344 PHE 0.014 0.001 PHE B 412 TYR 0.027 0.002 TYR F 274 ARG 0.008 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 828 time to evaluate : 5.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7939 (ttt) cc_final: 0.7511 (tmm) REVERT: A 244 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 388 HIS cc_start: 0.7682 (m170) cc_final: 0.7372 (m-70) REVERT: B 56 GLU cc_start: 0.8812 (pt0) cc_final: 0.8553 (pt0) REVERT: B 326 LYS cc_start: 0.8881 (ptpp) cc_final: 0.8548 (ptmm) REVERT: B 329 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: B 341 MET cc_start: 0.9038 (tmm) cc_final: 0.8699 (tmm) REVERT: B 378 GLN cc_start: 0.9236 (mp10) cc_final: 0.8963 (mp10) REVERT: B 415 MET cc_start: 0.9095 (tmm) cc_final: 0.8884 (tmm) REVERT: C 39 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8672 (tp) REVERT: C 59 GLN cc_start: 0.8466 (pm20) cc_final: 0.8111 (pp30) REVERT: C 218 GLU cc_start: 0.8426 (tp30) cc_final: 0.7955 (tp30) REVERT: C 234 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: C 326 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8216 (tttp) REVERT: D 13 GLU cc_start: 0.8753 (mp0) cc_final: 0.8484 (mp0) REVERT: D 21 MET cc_start: 0.8551 (ttm) cc_final: 0.8246 (ttt) REVERT: D 29 MET cc_start: 0.8557 (pmm) cc_final: 0.8219 (pmm) REVERT: D 109 ARG cc_start: 0.8388 (ptt90) cc_final: 0.8080 (ptt90) REVERT: D 218 GLU cc_start: 0.8580 (tp30) cc_final: 0.8188 (tp30) REVERT: D 322 ASP cc_start: 0.8843 (t0) cc_final: 0.8425 (t0) REVERT: D 326 LYS cc_start: 0.8754 (tppt) cc_final: 0.8400 (tppp) REVERT: E 29 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7324 (ptp) REVERT: E 87 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8695 (ttp80) REVERT: E 220 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: E 308 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8566 (mt-10) REVERT: E 329 GLU cc_start: 0.8285 (tp30) cc_final: 0.7829 (tp30) REVERT: E 401 ASN cc_start: 0.8805 (m-40) cc_final: 0.8522 (m-40) REVERT: F 29 MET cc_start: 0.4042 (ptt) cc_final: 0.3106 (ttp) REVERT: F 245 MET cc_start: 0.8886 (ppp) cc_final: 0.8662 (ppp) REVERT: F 334 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8790 (tm-30) REVERT: F 335 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8352 (t80) REVERT: F 342 GLU cc_start: 0.7633 (pp20) cc_final: 0.7126 (pp20) REVERT: F 369 GLU cc_start: 0.8873 (pp20) cc_final: 0.8494 (pm20) REVERT: F 405 MET cc_start: 0.9224 (ppp) cc_final: 0.8960 (ppp) REVERT: F 415 MET cc_start: 0.8215 (ppp) cc_final: 0.7781 (ppp) REVERT: I 406 THR cc_start: 0.6539 (OUTLIER) cc_final: 0.6250 (m) REVERT: I 416 MET cc_start: 0.3746 (ptt) cc_final: 0.3454 (ptt) REVERT: J 8 ASN cc_start: 0.8632 (m-40) cc_final: 0.8406 (m-40) REVERT: J 109 ARG cc_start: 0.8774 (mtm-85) cc_final: 0.8361 (mtm110) REVERT: J 110 TYR cc_start: 0.8586 (m-10) cc_final: 0.8329 (m-10) REVERT: J 136 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8526 (mp) REVERT: J 374 GLN cc_start: 0.8324 (tp40) cc_final: 0.7952 (tp40) REVERT: J 415 MET cc_start: 0.8866 (tmm) cc_final: 0.8501 (tpt) REVERT: K 1 MET cc_start: 0.7465 (tpt) cc_final: 0.7230 (tpp) REVERT: K 56 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8117 (tm-30) REVERT: K 57 ILE cc_start: 0.9542 (pt) cc_final: 0.9255 (mm) REVERT: L 85 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: L 88 ARG cc_start: 0.8588 (ptt-90) cc_final: 0.8330 (ptt180) REVERT: L 215 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8645 (mm-30) REVERT: L 220 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8139 (mp10) REVERT: L 322 ASP cc_start: 0.8861 (m-30) cc_final: 0.8584 (m-30) REVERT: L 326 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8621 (mmmm) REVERT: L 405 MET cc_start: 0.8820 (ptt) cc_final: 0.8089 (ppp) REVERT: M 58 LEU cc_start: 0.8578 (mm) cc_final: 0.8177 (mm) REVERT: M 72 TYR cc_start: 0.6966 (m-80) cc_final: 0.6750 (m-80) REVERT: M 219 MET cc_start: 0.8258 (mmt) cc_final: 0.7952 (tpp) REVERT: M 353 ARG cc_start: 0.8276 (mpp80) cc_final: 0.7992 (mpp80) REVERT: N 212 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7398 (mmp-170) REVERT: N 219 MET cc_start: 0.7498 (mmp) cc_final: 0.7149 (mmp) REVERT: N 342 GLU cc_start: 0.7255 (pp20) cc_final: 0.7038 (tm-30) REVERT: N 353 ARG cc_start: 0.5912 (mmp-170) cc_final: 0.5244 (mmp80) REVERT: N 374 GLN cc_start: 0.9011 (mp10) cc_final: 0.8810 (mp10) REVERT: N 375 GLU cc_start: 0.9089 (mp0) cc_final: 0.8806 (mp0) REVERT: N 388 HIS cc_start: 0.7231 (m-70) cc_final: 0.6775 (m-70) REVERT: N 405 MET cc_start: 0.8863 (ppp) cc_final: 0.8553 (ppp) REVERT: a 53 ASN cc_start: 0.8970 (m-40) cc_final: 0.8731 (t0) REVERT: a 83 ASP cc_start: 0.8135 (m-30) cc_final: 0.7718 (m-30) REVERT: a 146 ASP cc_start: 0.9021 (m-30) cc_final: 0.8748 (m-30) REVERT: b 83 ASP cc_start: 0.8754 (t0) cc_final: 0.8491 (t0) REVERT: b 116 ASN cc_start: 0.8747 (m-40) cc_final: 0.8264 (p0) REVERT: b 128 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9129 (mm-30) REVERT: c 141 ASN cc_start: 0.9272 (t0) cc_final: 0.8960 (t0) REVERT: d 104 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8646 (mm) REVERT: d 183 GLN cc_start: 0.9295 (tp40) cc_final: 0.9019 (tp40) REVERT: e 89 MET cc_start: 0.8253 (tmm) cc_final: 0.7591 (tmm) REVERT: e 120 GLN cc_start: 0.8812 (tp-100) cc_final: 0.8509 (tp40) REVERT: e 168 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8597 (mmmt) REVERT: e 183 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8801 (tm-30) REVERT: f 83 ASP cc_start: 0.8781 (m-30) cc_final: 0.8219 (m-30) REVERT: f 139 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8902 (tmtt) REVERT: g 142 TYR cc_start: 0.8388 (m-80) cc_final: 0.8105 (m-80) REVERT: h 49 ASP cc_start: 0.9052 (m-30) cc_final: 0.8721 (m-30) REVERT: h 50 GLU cc_start: 0.8957 (pp20) cc_final: 0.8584 (pp20) REVERT: h 71 ARG cc_start: 0.8753 (mpp80) cc_final: 0.8116 (mtm-85) REVERT: h 74 GLU cc_start: 0.8946 (tp30) cc_final: 0.8638 (tp30) REVERT: i 141 ASN cc_start: 0.8701 (t0) cc_final: 0.8310 (t0) REVERT: j 56 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7850 (mt-10) REVERT: j 69 TYR cc_start: 0.7510 (t80) cc_final: 0.7264 (t80) REVERT: j 138 GLU cc_start: 0.7925 (pp20) cc_final: 0.7125 (pm20) REVERT: j 153 ILE cc_start: 0.7969 (mm) cc_final: 0.7563 (tp) REVERT: j 175 MET cc_start: 0.8411 (pmm) cc_final: 0.8157 (pmm) REVERT: j 179 ARG cc_start: 0.8539 (tpp-160) cc_final: 0.8037 (tpm170) outliers start: 140 outliers final: 93 residues processed: 914 average time/residue: 0.5195 time to fit residues: 793.4907 Evaluate side-chains 875 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 770 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain I residue 388 HIS Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 393 ILE Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 326 LYS Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain N residue 212 ARG Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 372 THR Chi-restraints excluded: chain N residue 378 GLN Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 59 LYS Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 170 THR Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 83 ASP Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain e residue 17 LYS Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 136 LYS Chi-restraints excluded: chain f residue 168 LYS Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain h residue 96 LEU Chi-restraints excluded: chain h residue 119 ILE Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 175 MET Chi-restraints excluded: chain j residue 116 ASN Chi-restraints excluded: chain j residue 117 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 400 optimal weight: 2.9990 chunk 258 optimal weight: 7.9990 chunk 386 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 411 optimal weight: 20.0000 chunk 441 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 509 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 292 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 GLN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN ** K 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 GLN N 172 GLN ** a 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 55539 Z= 0.281 Angle : 0.699 15.317 74914 Z= 0.357 Chirality : 0.045 0.229 8490 Planarity : 0.004 0.052 9757 Dihedral : 6.487 63.757 7791 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.35 % Allowed : 17.61 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.10), residues: 6854 helix: 1.55 (0.08), residues: 3794 sheet: 0.07 (0.19), residues: 724 loop : -0.37 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP g 133 HIS 0.011 0.001 HIS J 344 PHE 0.019 0.001 PHE I 398 TYR 0.019 0.002 TYR a 107 ARG 0.010 0.000 ARG K 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 786 time to evaluate : 5.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7990 (ttt) cc_final: 0.7495 (tmm) REVERT: A 244 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 388 HIS cc_start: 0.7722 (m170) cc_final: 0.7390 (m90) REVERT: B 245 MET cc_start: 0.9008 (tpp) cc_final: 0.8678 (tpp) REVERT: B 326 LYS cc_start: 0.8901 (ptpp) cc_final: 0.8455 (mtpp) REVERT: B 329 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: B 341 MET cc_start: 0.9068 (tmm) cc_final: 0.8680 (tmm) REVERT: B 378 GLN cc_start: 0.9249 (mp10) cc_final: 0.8974 (mp10) REVERT: C 23 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8350 (mm) REVERT: C 39 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8735 (tp) REVERT: C 218 GLU cc_start: 0.8481 (tp30) cc_final: 0.8039 (tp30) REVERT: C 234 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8700 (mt-10) REVERT: C 326 LYS cc_start: 0.8561 (ptmm) cc_final: 0.7763 (tttp) REVERT: D 13 GLU cc_start: 0.8748 (mp0) cc_final: 0.8467 (mp0) REVERT: D 21 MET cc_start: 0.8430 (ttm) cc_final: 0.7925 (ttt) REVERT: D 29 MET cc_start: 0.8510 (pmm) cc_final: 0.8141 (pmm) REVERT: D 109 ARG cc_start: 0.8437 (ptt90) cc_final: 0.8131 (ptt90) REVERT: D 218 GLU cc_start: 0.8593 (tp30) cc_final: 0.8218 (tp30) REVERT: D 322 ASP cc_start: 0.8848 (t0) cc_final: 0.8440 (t0) REVERT: D 326 LYS cc_start: 0.8807 (tppt) cc_final: 0.8524 (mmmm) REVERT: D 392 GLU cc_start: 0.8325 (pm20) cc_final: 0.7557 (pt0) REVERT: E 29 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7376 (ptp) REVERT: E 87 ARG cc_start: 0.9098 (ttp80) cc_final: 0.8720 (ttp80) REVERT: E 220 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: E 329 GLU cc_start: 0.8374 (tp30) cc_final: 0.7891 (tp30) REVERT: E 401 ASN cc_start: 0.8796 (m-40) cc_final: 0.8527 (m-40) REVERT: F 241 GLN cc_start: 0.8678 (pp30) cc_final: 0.8417 (pm20) REVERT: F 334 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8777 (tm-30) REVERT: F 335 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8372 (t80) REVERT: F 369 GLU cc_start: 0.8937 (pp20) cc_final: 0.8567 (pm20) REVERT: F 405 MET cc_start: 0.9213 (ppp) cc_final: 0.8960 (ppp) REVERT: F 415 MET cc_start: 0.8222 (ppp) cc_final: 0.7862 (ppp) REVERT: I 29 MET cc_start: 0.7017 (ppp) cc_final: 0.6584 (tmm) REVERT: I 327 MET cc_start: 0.7595 (ptm) cc_final: 0.7376 (ptt) REVERT: I 406 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6225 (m) REVERT: I 416 MET cc_start: 0.3617 (ptt) cc_final: 0.3283 (ptt) REVERT: J 8 ASN cc_start: 0.8487 (m-40) cc_final: 0.8214 (m-40) REVERT: J 109 ARG cc_start: 0.8783 (mtm-85) cc_final: 0.8357 (mtm110) REVERT: J 110 TYR cc_start: 0.8618 (m-10) cc_final: 0.8366 (m-10) REVERT: J 132 LEU cc_start: 0.8102 (mp) cc_final: 0.7883 (mp) REVERT: J 415 MET cc_start: 0.8905 (tmm) cc_final: 0.7948 (tpt) REVERT: J 418 ARG cc_start: 0.9220 (ptt90) cc_final: 0.8957 (ptt180) REVERT: K 1 MET cc_start: 0.7441 (tpt) cc_final: 0.7240 (tpp) REVERT: K 56 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8108 (tm-30) REVERT: K 57 ILE cc_start: 0.9530 (pt) cc_final: 0.9284 (mm) REVERT: K 90 ASN cc_start: 0.8281 (t0) cc_final: 0.7682 (t0) REVERT: L 85 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: L 215 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8681 (mm-30) REVERT: L 220 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: L 234 GLU cc_start: 0.8238 (pm20) cc_final: 0.7818 (pm20) REVERT: L 322 ASP cc_start: 0.8876 (m-30) cc_final: 0.8595 (m-30) REVERT: L 326 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8644 (mmmm) REVERT: M 58 LEU cc_start: 0.8586 (mm) cc_final: 0.8217 (mm) REVERT: M 193 GLN cc_start: 0.8779 (tt0) cc_final: 0.8491 (tt0) REVERT: M 219 MET cc_start: 0.8371 (mmt) cc_final: 0.8002 (tpp) REVERT: N 219 MET cc_start: 0.7556 (mmp) cc_final: 0.7220 (mmp) REVERT: N 342 GLU cc_start: 0.7257 (pp20) cc_final: 0.7020 (tm-30) REVERT: N 343 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7916 (mm) REVERT: N 374 GLN cc_start: 0.9063 (mp10) cc_final: 0.8849 (mp10) REVERT: N 375 GLU cc_start: 0.9120 (mp0) cc_final: 0.8833 (mp0) REVERT: N 388 HIS cc_start: 0.7215 (m-70) cc_final: 0.6753 (m-70) REVERT: N 405 MET cc_start: 0.8858 (ppp) cc_final: 0.8657 (ppp) REVERT: a 50 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7612 (tm-30) REVERT: a 53 ASN cc_start: 0.8976 (m-40) cc_final: 0.8743 (t0) REVERT: a 83 ASP cc_start: 0.8181 (m-30) cc_final: 0.7757 (m-30) REVERT: a 146 ASP cc_start: 0.9041 (m-30) cc_final: 0.8736 (m-30) REVERT: b 83 ASP cc_start: 0.8769 (t0) cc_final: 0.8561 (t0) REVERT: b 116 ASN cc_start: 0.8782 (m-40) cc_final: 0.8311 (p0) REVERT: b 128 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9146 (mm-30) REVERT: c 141 ASN cc_start: 0.9273 (t0) cc_final: 0.8991 (t0) REVERT: d 104 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8647 (mm) REVERT: d 183 GLN cc_start: 0.9297 (tp40) cc_final: 0.8873 (tm-30) REVERT: e 89 MET cc_start: 0.8216 (tmm) cc_final: 0.7630 (tmm) REVERT: e 120 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8578 (tp40) REVERT: e 168 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8718 (mmmt) REVERT: e 183 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8817 (tm-30) REVERT: f 83 ASP cc_start: 0.8795 (m-30) cc_final: 0.8179 (m-30) REVERT: f 139 LYS cc_start: 0.9113 (tmtt) cc_final: 0.8907 (tmtt) REVERT: g 142 TYR cc_start: 0.8409 (m-80) cc_final: 0.8026 (m-80) REVERT: h 49 ASP cc_start: 0.9058 (m-30) cc_final: 0.8734 (m-30) REVERT: h 50 GLU cc_start: 0.8971 (pp20) cc_final: 0.8575 (pp20) REVERT: h 71 ARG cc_start: 0.8761 (mpp80) cc_final: 0.8115 (mtm-85) REVERT: h 74 GLU cc_start: 0.8964 (tp30) cc_final: 0.8646 (tp30) REVERT: h 168 LYS cc_start: 0.8957 (mptt) cc_final: 0.8641 (mptt) REVERT: i 141 ASN cc_start: 0.8746 (t0) cc_final: 0.8367 (t0) REVERT: j 56 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7892 (mt-10) REVERT: j 103 GLU cc_start: 0.7883 (mp0) cc_final: 0.7645 (mp0) REVERT: j 138 GLU cc_start: 0.7888 (pp20) cc_final: 0.6955 (pm20) REVERT: j 175 MET cc_start: 0.8461 (pmm) cc_final: 0.8189 (pmm) REVERT: j 179 ARG cc_start: 0.8530 (tpp-160) cc_final: 0.8029 (tpm170) outliers start: 137 outliers final: 102 residues processed: 874 average time/residue: 0.5343 time to fit residues: 785.8377 Evaluate side-chains 876 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 762 time to evaluate : 4.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain F residue 388 HIS Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 360 TYR Chi-restraints excluded: chain I residue 388 HIS Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 393 ILE Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 326 LYS Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 205 MET Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 162 LEU Chi-restraints excluded: chain M residue 245 MET Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 411 ASP Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 343 LEU Chi-restraints excluded: chain N residue 372 THR Chi-restraints excluded: chain N residue 378 GLN Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 59 LYS Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 170 THR Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 50 GLU Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 83 ASP Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain e residue 17 LYS Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 136 LYS Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain g residue 162 VAL Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain h residue 96 LEU Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 175 MET Chi-restraints excluded: chain j residue 50 GLU Chi-restraints excluded: chain j residue 116 ASN Chi-restraints excluded: chain j residue 117 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 589 optimal weight: 0.7980 chunk 620 optimal weight: 6.9990 chunk 566 optimal weight: 4.9990 chunk 603 optimal weight: 0.0170 chunk 363 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 473 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 545 optimal weight: 0.9990 chunk 570 optimal weight: 5.9990 chunk 601 optimal weight: 0.8980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 GLN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN ** K 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN ** a 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 16 ASN g 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 55539 Z= 0.195 Angle : 0.701 15.110 74914 Z= 0.356 Chirality : 0.044 0.228 8490 Planarity : 0.004 0.052 9757 Dihedral : 6.330 61.046 7791 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.02 % Allowed : 17.97 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.10), residues: 6854 helix: 1.54 (0.08), residues: 3794 sheet: 0.16 (0.19), residues: 716 loop : -0.37 (0.13), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP i 133 HIS 0.014 0.001 HIS I 256 PHE 0.020 0.001 PHE B 412 TYR 0.028 0.001 TYR c 107 ARG 0.011 0.000 ARG i 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 828 time to evaluate : 5.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8021 (ttt) cc_final: 0.7493 (tmm) REVERT: A 244 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 274 TYR cc_start: 0.9079 (m-80) cc_final: 0.8117 (m-80) REVERT: A 388 HIS cc_start: 0.7770 (m170) cc_final: 0.7412 (m90) REVERT: B 219 MET cc_start: 0.9237 (tpt) cc_final: 0.9009 (tpt) REVERT: B 326 LYS cc_start: 0.8886 (ptpp) cc_final: 0.8448 (mtpp) REVERT: B 329 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: B 333 GLU cc_start: 0.8951 (pt0) cc_final: 0.8723 (tt0) REVERT: B 341 MET cc_start: 0.9064 (tmm) cc_final: 0.8693 (tmm) REVERT: B 378 GLN cc_start: 0.9236 (mp10) cc_final: 0.8942 (mp10) REVERT: C 23 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8306 (mm) REVERT: C 39 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8676 (tp) REVERT: C 59 GLN cc_start: 0.8491 (pm20) cc_final: 0.8126 (pp30) REVERT: C 218 GLU cc_start: 0.8465 (tp30) cc_final: 0.8042 (tp30) REVERT: C 234 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8601 (mt-10) REVERT: C 248 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8762 (mm-30) REVERT: C 326 LYS cc_start: 0.8499 (ptmm) cc_final: 0.8061 (tttp) REVERT: D 13 GLU cc_start: 0.8734 (mp0) cc_final: 0.8450 (mp0) REVERT: D 21 MET cc_start: 0.8450 (ttm) cc_final: 0.7912 (ttt) REVERT: D 29 MET cc_start: 0.8542 (pmm) cc_final: 0.8175 (pmm) REVERT: D 109 ARG cc_start: 0.8393 (ptt90) cc_final: 0.8065 (ptt90) REVERT: D 218 GLU cc_start: 0.8562 (tp30) cc_final: 0.8180 (tp30) REVERT: D 322 ASP cc_start: 0.8818 (t0) cc_final: 0.8401 (t0) REVERT: D 326 LYS cc_start: 0.8794 (tppt) cc_final: 0.8522 (tppp) REVERT: E 29 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7369 (ptp) REVERT: E 220 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: E 308 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8601 (mt-10) REVERT: E 329 GLU cc_start: 0.8317 (tp30) cc_final: 0.7862 (tp30) REVERT: E 401 ASN cc_start: 0.8758 (m-40) cc_final: 0.8487 (m-40) REVERT: F 29 MET cc_start: 0.4677 (ptt) cc_final: 0.3714 (tmm) REVERT: F 88 ARG cc_start: 0.8677 (ptt90) cc_final: 0.8109 (ptt90) REVERT: F 334 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8808 (tm-30) REVERT: F 335 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8363 (t80) REVERT: F 342 GLU cc_start: 0.7530 (pp20) cc_final: 0.7072 (pp20) REVERT: F 369 GLU cc_start: 0.8911 (pp20) cc_final: 0.8522 (pm20) REVERT: F 405 MET cc_start: 0.9186 (ppp) cc_final: 0.8937 (ppp) REVERT: F 415 MET cc_start: 0.8188 (ppp) cc_final: 0.7869 (ppp) REVERT: I 29 MET cc_start: 0.6934 (ppp) cc_final: 0.6495 (tmm) REVERT: I 327 MET cc_start: 0.7542 (ptm) cc_final: 0.7331 (ptt) REVERT: I 406 THR cc_start: 0.6497 (OUTLIER) cc_final: 0.6196 (m) REVERT: I 416 MET cc_start: 0.3601 (ptt) cc_final: 0.3287 (ptt) REVERT: J 8 ASN cc_start: 0.8585 (m-40) cc_final: 0.8305 (m110) REVERT: J 109 ARG cc_start: 0.8764 (mtm-85) cc_final: 0.8318 (mtm110) REVERT: J 110 TYR cc_start: 0.8569 (m-10) cc_final: 0.8304 (m-10) REVERT: J 234 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: J 415 MET cc_start: 0.8913 (tmm) cc_final: 0.7991 (tpt) REVERT: J 418 ARG cc_start: 0.9223 (ptt90) cc_final: 0.8970 (ptt180) REVERT: K 56 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8114 (tm-30) REVERT: K 57 ILE cc_start: 0.9516 (pt) cc_final: 0.9296 (mm) REVERT: K 90 ASN cc_start: 0.8333 (t0) cc_final: 0.7718 (t0) REVERT: L 215 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8683 (mm-30) REVERT: L 220 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: L 234 GLU cc_start: 0.8212 (pm20) cc_final: 0.7819 (pm20) REVERT: L 322 ASP cc_start: 0.8848 (m-30) cc_final: 0.8572 (m-30) REVERT: L 326 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8638 (mmmm) REVERT: M 58 LEU cc_start: 0.8584 (mm) cc_final: 0.8194 (mm) REVERT: M 72 TYR cc_start: 0.6753 (m-80) cc_final: 0.6504 (m-80) REVERT: M 193 GLN cc_start: 0.8743 (tt0) cc_final: 0.8469 (tt0) REVERT: M 219 MET cc_start: 0.8272 (mmt) cc_final: 0.7955 (tpp) REVERT: N 219 MET cc_start: 0.7472 (mmp) cc_final: 0.7129 (mmp) REVERT: N 343 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7723 (mm) REVERT: N 353 ARG cc_start: 0.5947 (mmp-170) cc_final: 0.5258 (mmp80) REVERT: N 388 HIS cc_start: 0.7120 (m-70) cc_final: 0.6662 (m-70) REVERT: N 405 MET cc_start: 0.8828 (ppp) cc_final: 0.8549 (ppp) REVERT: a 50 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7622 (tm-30) REVERT: a 53 ASN cc_start: 0.8939 (m-40) cc_final: 0.8731 (t0) REVERT: a 83 ASP cc_start: 0.8154 (m-30) cc_final: 0.7742 (m-30) REVERT: a 146 ASP cc_start: 0.9010 (m-30) cc_final: 0.8711 (m-30) REVERT: b 116 ASN cc_start: 0.8782 (m-40) cc_final: 0.8305 (p0) REVERT: b 128 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9139 (mm-30) REVERT: c 141 ASN cc_start: 0.9260 (t0) cc_final: 0.9011 (t0) REVERT: d 104 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8599 (mm) REVERT: d 183 GLN cc_start: 0.9276 (tp40) cc_final: 0.8861 (tm-30) REVERT: e 89 MET cc_start: 0.8212 (tmm) cc_final: 0.7812 (tmm) REVERT: e 120 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8520 (tp40) REVERT: e 168 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8701 (mmmt) REVERT: e 183 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8812 (tm-30) REVERT: f 83 ASP cc_start: 0.8805 (m-30) cc_final: 0.8223 (m-30) REVERT: g 142 TYR cc_start: 0.8407 (m-80) cc_final: 0.8080 (m-80) REVERT: h 49 ASP cc_start: 0.9053 (m-30) cc_final: 0.8749 (m-30) REVERT: h 50 GLU cc_start: 0.8970 (pp20) cc_final: 0.8577 (pp20) REVERT: h 71 ARG cc_start: 0.8752 (mpp80) cc_final: 0.8105 (mtm-85) REVERT: h 74 GLU cc_start: 0.8955 (tp30) cc_final: 0.8640 (tp30) REVERT: h 168 LYS cc_start: 0.8973 (mptt) cc_final: 0.8663 (mptt) REVERT: i 141 ASN cc_start: 0.8721 (t0) cc_final: 0.8341 (t0) REVERT: i 168 LYS cc_start: 0.8945 (mmpt) cc_final: 0.8666 (mmmt) REVERT: j 56 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7962 (mt-10) REVERT: j 153 ILE cc_start: 0.7929 (mm) cc_final: 0.7627 (tp) REVERT: j 175 MET cc_start: 0.8472 (pmm) cc_final: 0.7987 (pmm) outliers start: 118 outliers final: 88 residues processed: 902 average time/residue: 0.5137 time to fit residues: 775.6566 Evaluate side-chains 872 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 772 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 388 HIS Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 393 ILE Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 326 LYS Chi-restraints excluded: chain K residue 327 MET Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 343 LEU Chi-restraints excluded: chain N residue 372 THR Chi-restraints excluded: chain N residue 378 GLN Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 170 THR Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 83 ASP Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain e residue 17 LYS Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 136 LYS Chi-restraints excluded: chain f residue 168 LYS Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain h residue 96 LEU Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 147 SER Chi-restraints excluded: chain i residue 175 MET Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 116 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 396 optimal weight: 4.9990 chunk 638 optimal weight: 0.9980 chunk 389 optimal weight: 3.9990 chunk 302 optimal weight: 4.9990 chunk 443 optimal weight: 1.9990 chunk 669 optimal weight: 7.9990 chunk 616 optimal weight: 0.8980 chunk 533 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 411 optimal weight: 20.0000 chunk 326 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN ** K 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 GLN ** b 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 55539 Z= 0.256 Angle : 0.723 15.150 74914 Z= 0.368 Chirality : 0.045 0.301 8490 Planarity : 0.004 0.052 9757 Dihedral : 6.402 63.147 7791 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.87 % Allowed : 18.17 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.10), residues: 6854 helix: 1.53 (0.08), residues: 3795 sheet: 0.12 (0.19), residues: 716 loop : -0.37 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP g 133 HIS 0.011 0.001 HIS I 256 PHE 0.017 0.001 PHE B 412 TYR 0.032 0.002 TYR c 107 ARG 0.009 0.000 ARG F 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13708 Ramachandran restraints generated. 6854 Oldfield, 0 Emsley, 6854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 789 time to evaluate : 5.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8003 (ttt) cc_final: 0.7568 (tmm) REVERT: A 244 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 274 TYR cc_start: 0.9040 (m-80) cc_final: 0.8111 (m-80) REVERT: A 388 HIS cc_start: 0.7873 (m170) cc_final: 0.7542 (m90) REVERT: B 44 LYS cc_start: 0.8755 (pttm) cc_final: 0.8418 (mmtt) REVERT: B 219 MET cc_start: 0.9237 (tpt) cc_final: 0.9006 (tpt) REVERT: B 326 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8468 (mtpp) REVERT: B 329 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8528 (pm20) REVERT: B 341 MET cc_start: 0.9083 (tmm) cc_final: 0.8669 (tmm) REVERT: B 378 GLN cc_start: 0.9258 (mp10) cc_final: 0.8962 (mp10) REVERT: C 23 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8297 (mm) REVERT: C 39 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8715 (tp) REVERT: C 218 GLU cc_start: 0.8468 (tp30) cc_final: 0.8028 (tp30) REVERT: C 234 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8636 (mt-10) REVERT: C 248 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8832 (mm-30) REVERT: C 326 LYS cc_start: 0.8450 (ptmm) cc_final: 0.7994 (tttp) REVERT: D 13 GLU cc_start: 0.8741 (mp0) cc_final: 0.8449 (mp0) REVERT: D 21 MET cc_start: 0.8458 (ttm) cc_final: 0.7953 (ttt) REVERT: D 29 MET cc_start: 0.8545 (pmm) cc_final: 0.8168 (pmm) REVERT: D 109 ARG cc_start: 0.8401 (ptt90) cc_final: 0.8072 (ptt90) REVERT: D 218 GLU cc_start: 0.8576 (tp30) cc_final: 0.8193 (tp30) REVERT: D 322 ASP cc_start: 0.8848 (t0) cc_final: 0.8434 (t0) REVERT: D 326 LYS cc_start: 0.8807 (tppt) cc_final: 0.8531 (tppp) REVERT: D 392 GLU cc_start: 0.8299 (pm20) cc_final: 0.7431 (pt0) REVERT: E 29 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7401 (ptp) REVERT: E 220 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8017 (mt0) REVERT: E 308 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8620 (mt-10) REVERT: E 329 GLU cc_start: 0.8371 (tp30) cc_final: 0.7885 (tp30) REVERT: E 401 ASN cc_start: 0.8792 (m-40) cc_final: 0.8498 (m-40) REVERT: F 29 MET cc_start: 0.4685 (ptt) cc_final: 0.3384 (tmm) REVERT: F 241 GLN cc_start: 0.8587 (pp30) cc_final: 0.8312 (pm20) REVERT: F 334 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8790 (tm-30) REVERT: F 335 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8374 (t80) REVERT: F 369 GLU cc_start: 0.8947 (pp20) cc_final: 0.8552 (pm20) REVERT: F 405 MET cc_start: 0.9199 (ppp) cc_final: 0.8948 (ppp) REVERT: F 415 MET cc_start: 0.8218 (ppp) cc_final: 0.7925 (ppp) REVERT: I 327 MET cc_start: 0.7637 (ptm) cc_final: 0.7430 (ptt) REVERT: I 406 THR cc_start: 0.6462 (OUTLIER) cc_final: 0.6151 (m) REVERT: I 416 MET cc_start: 0.3642 (ptt) cc_final: 0.3310 (ptt) REVERT: J 8 ASN cc_start: 0.8481 (m-40) cc_final: 0.8169 (m110) REVERT: J 109 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8311 (mtm110) REVERT: J 110 TYR cc_start: 0.8589 (m-10) cc_final: 0.8327 (m-10) REVERT: J 234 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: J 415 MET cc_start: 0.8946 (tmm) cc_final: 0.7993 (tpt) REVERT: J 418 ARG cc_start: 0.9223 (ptt90) cc_final: 0.8973 (ptt180) REVERT: K 56 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8129 (tm-30) REVERT: K 90 ASN cc_start: 0.8370 (t0) cc_final: 0.7815 (t0) REVERT: L 215 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8688 (mm-30) REVERT: L 220 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8149 (mp10) REVERT: L 234 GLU cc_start: 0.8193 (pm20) cc_final: 0.7758 (pm20) REVERT: L 322 ASP cc_start: 0.8865 (m-30) cc_final: 0.8589 (m-30) REVERT: L 326 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8591 (mmmm) REVERT: M 58 LEU cc_start: 0.8576 (mm) cc_final: 0.8214 (mm) REVERT: M 72 TYR cc_start: 0.6712 (m-80) cc_final: 0.6483 (m-80) REVERT: M 193 GLN cc_start: 0.8773 (tt0) cc_final: 0.8484 (tt0) REVERT: M 219 MET cc_start: 0.8318 (mmt) cc_final: 0.7985 (tpp) REVERT: M 353 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8220 (mpp80) REVERT: N 219 MET cc_start: 0.7535 (mmp) cc_final: 0.7189 (mmp) REVERT: N 241 GLN cc_start: 0.8771 (pm20) cc_final: 0.8459 (pm20) REVERT: N 353 ARG cc_start: 0.6007 (mmp-170) cc_final: 0.5382 (mmp80) REVERT: N 388 HIS cc_start: 0.7082 (m-70) cc_final: 0.6557 (m-70) REVERT: a 50 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7632 (tm-30) REVERT: a 83 ASP cc_start: 0.8145 (m-30) cc_final: 0.7712 (m-30) REVERT: a 146 ASP cc_start: 0.9029 (m-30) cc_final: 0.8722 (m-30) REVERT: b 105 MET cc_start: 0.8235 (mmp) cc_final: 0.7983 (mmm) REVERT: b 116 ASN cc_start: 0.8774 (m-40) cc_final: 0.8337 (p0) REVERT: b 128 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9159 (mm-30) REVERT: c 141 ASN cc_start: 0.9270 (t0) cc_final: 0.8987 (t0) REVERT: d 31 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8664 (tm-30) REVERT: d 89 MET cc_start: 0.8280 (tpt) cc_final: 0.7961 (tmm) REVERT: d 104 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8586 (mm) REVERT: d 183 GLN cc_start: 0.9283 (tp40) cc_final: 0.8867 (tm-30) REVERT: e 89 MET cc_start: 0.8203 (tmm) cc_final: 0.7863 (tmm) REVERT: e 120 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8578 (tp40) REVERT: e 168 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8705 (mmmt) REVERT: e 183 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8823 (tm-30) REVERT: f 83 ASP cc_start: 0.8812 (m-30) cc_final: 0.8219 (m-30) REVERT: g 142 TYR cc_start: 0.8425 (m-80) cc_final: 0.8096 (m-80) REVERT: h 49 ASP cc_start: 0.9062 (m-30) cc_final: 0.8765 (m-30) REVERT: h 50 GLU cc_start: 0.8972 (pp20) cc_final: 0.8573 (pp20) REVERT: h 71 ARG cc_start: 0.8762 (mpp80) cc_final: 0.8118 (mtm-85) REVERT: h 74 GLU cc_start: 0.8965 (tp30) cc_final: 0.8652 (tp30) REVERT: h 168 LYS cc_start: 0.8992 (mptt) cc_final: 0.8664 (mptt) REVERT: i 141 ASN cc_start: 0.8736 (t0) cc_final: 0.8353 (t0) REVERT: i 168 LYS cc_start: 0.8934 (mmpt) cc_final: 0.8658 (mmmt) REVERT: j 56 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7999 (mt-10) REVERT: j 153 ILE cc_start: 0.7966 (mm) cc_final: 0.7683 (tp) REVERT: j 175 MET cc_start: 0.8487 (pmm) cc_final: 0.8009 (pmm) REVERT: j 179 ARG cc_start: 0.8562 (tpp-160) cc_final: 0.8193 (tpm170) outliers start: 109 outliers final: 89 residues processed: 855 average time/residue: 0.5365 time to fit residues: 767.9854 Evaluate side-chains 865 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 765 time to evaluate : 5.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 64 PHE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 378 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 335 PHE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 388 HIS Chi-restraints excluded: chain I residue 406 THR Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 314 THR Chi-restraints excluded: chain J residue 393 ILE Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 326 LYS Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain L residue 205 MET Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 411 ASP Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 372 THR Chi-restraints excluded: chain N residue 378 GLN Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 170 THR Chi-restraints excluded: chain b residue 94 THR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 131 LEU Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 83 ASP Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain e residue 17 LYS Chi-restraints excluded: chain f residue 35 LEU Chi-restraints excluded: chain f residue 44 ASN Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 136 LYS Chi-restraints excluded: chain f residue 168 LYS Chi-restraints excluded: chain g residue 53 ASN Chi-restraints excluded: chain h residue 53 ASN Chi-restraints excluded: chain h residue 83 ASP Chi-restraints excluded: chain i residue 35 LEU Chi-restraints excluded: chain i residue 78 HIS Chi-restraints excluded: chain i residue 147 SER Chi-restraints excluded: chain i residue 175 MET Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain j residue 116 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 672 random chunks: chunk 423 optimal weight: 6.9990 chunk 567 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 491 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 533 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 548 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 292 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 ASN J 8 ASN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN ** K 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 HIS ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.102405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.073436 restraints weight = 174692.322| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.82 r_work: 0.3152 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 55539 Z= 0.200 Angle : 0.725 15.141 74914 Z= 0.368 Chirality : 0.044 0.306 8490 Planarity : 0.004 0.052 9757 Dihedral : 6.280 61.275 7791 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.94 % Allowed : 18.40 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 6854 helix: 1.55 (0.08), residues: 3792 sheet: 0.20 (0.20), residues: 703 loop : -0.37 (0.13), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP g 133 HIS 0.011 0.001 HIS J 344 PHE 0.015 0.001 PHE M 89 TYR 0.028 0.002 TYR c 107 ARG 0.011 0.000 ARG E 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14357.23 seconds wall clock time: 250 minutes 50.64 seconds (15050.64 seconds total)