Starting phenix.real_space_refine on Sat Mar 23 11:40:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbt_27306/03_2024/8dbt_27306_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbt_27306/03_2024/8dbt_27306.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/8dbt_27306/03_2024/8dbt_27306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbt_27306/03_2024/8dbt_27306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbt_27306/03_2024/8dbt_27306_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbt_27306/03_2024/8dbt_27306_updated.pdb" } 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= -0.000 sd= 0.002 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 16 5.49 5 Mg 5 5.21 5 S 179 5.16 5 C 23463 2.51 5 N 6312 2.21 5 O 6962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E GLU 369": "OE1" <-> "OE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F GLU 36": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F GLU 280": "OE1" <-> "OE2" Residue "F GLU 385": "OE1" <-> "OE2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F GLU 432": "OE1" <-> "OE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "G GLU 278": "OE1" <-> "OE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W GLU 36": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W GLU 103": "OE1" <-> "OE2" Residue "W GLU 118": "OE1" <-> "OE2" Residue "W ARG 164": "NH1" <-> "NH2" Residue "W ARG 169": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "M ASP 44": "OD1" <-> "OD2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 41": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X ARG 83": "NH1" <-> "NH2" Residue "X GLU 89": "OE1" <-> "OE2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X GLU 108": "OE1" <-> "OE2" Residue "X GLU 110": "OE1" <-> "OE2" Residue "X ARG 113": "NH1" <-> "NH2" Residue "X ARG 115": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 48": "OE1" <-> "OE2" Residue "Y GLU 77": "OE1" <-> "OE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ARG 98": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Y GLU 133": "OE1" <-> "OE2" Residue "Y GLU 137": "OE1" <-> "OE2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "a TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 80": "OE1" <-> "OE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36937 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3826 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 18, 'TRANS': 491} Chain: "D" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1021 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.39, per 1000 atoms: 0.47 Number of scatterers: 36937 At special positions: 0 Unit cell: (180.193, 219.037, 134.875, 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 179 16.00 P 16 15.00 Mg 5 11.99 O 6962 8.00 N 6312 7.00 C 23463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.51 Conformation dependent library (CDL) restraints added in 6.9 seconds 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8810 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 26 sheets defined 56.2% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.94 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 188 removed outlier: 3.964A pdb=" N ARG A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 252 Proline residue: A 239 - end of helix removed outlier: 3.945A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.944A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 293 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 295 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 407 removed outlier: 3.536A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 441 through 452 removed outlier: 3.548A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.538A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 478 " --> pdb=" O TYR A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'B' and resid 2 through 18 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.532A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 238 through 252 removed outlier: 3.611A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.985A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER B 295 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 384 through 406 removed outlier: 4.880A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 478 removed outlier: 4.079A pdb=" N GLY B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.853A pdb=" N ARG C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 238 through 252 removed outlier: 3.740A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.645A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER C 295 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 409 removed outlier: 4.125A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N PHE C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 3.725A pdb=" N ILE C 464 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 475 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.877A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 155 through 169 removed outlier: 4.065A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 213 through 232 removed outlier: 4.773A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.581A pdb=" N ALA D 250 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU D 253 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 255 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 281 removed outlier: 3.533A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG D 281 " --> pdb=" O VAL D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 306 through 314 removed outlier: 4.310A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 removed outlier: 3.626A pdb=" N LEU D 328 " --> pdb=" O GLN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 351 through 377 removed outlier: 4.338A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.665A pdb=" N LYS D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 removed outlier: 3.669A pdb=" N GLU D 408 " --> pdb=" O PHE D 405 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL D 409 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D 411 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.869A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 155 through 169 removed outlier: 3.653A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 213 through 232 removed outlier: 3.545A pdb=" N ARG E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 257 removed outlier: 3.583A pdb=" N VAL E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 281 removed outlier: 4.112A pdb=" N ARG E 281 " --> pdb=" O VAL E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 306 through 314 removed outlier: 4.596A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS E 314 " --> pdb=" O THR E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 removed outlier: 4.177A pdb=" N LEU E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 377 removed outlier: 7.735A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 384 through 399 removed outlier: 3.593A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 433 through 435 No H-bonds generated for 'chain 'E' and resid 433 through 435' Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.763A pdb=" N VAL E 453 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 131 through 136 Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 213 through 232 removed outlier: 4.888A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 271 through 279 removed outlier: 3.518A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.657A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 351 through 376 removed outlier: 4.084A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.646A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 420 through 432 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 449 through 456 removed outlier: 3.905A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 55 removed outlier: 4.314A pdb=" N GLU G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 91 through 108 removed outlier: 3.969A pdb=" N LYS G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 149 through 160 removed outlier: 3.867A pdb=" N VAL G 154 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU G 156 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'G' and resid 211 through 282 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 91 through 107 Processing helix chain 'H' and resid 111 through 135 removed outlier: 3.659A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS H 135 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 20 removed outlier: 3.911A pdb=" N ARG W 8 " --> pdb=" O THR W 5 " (cutoff:3.500A) Proline residue: W 9 - end of helix removed outlier: 3.742A pdb=" N LYS W 12 " --> pdb=" O PRO W 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA W 14 " --> pdb=" O ALA W 11 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE W 17 " --> pdb=" O ALA W 14 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 39 removed outlier: 3.551A pdb=" N PHE W 33 " --> pdb=" O ASP W 29 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 47 Processing helix chain 'W' and resid 53 through 63 removed outlier: 3.679A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 81 Processing helix chain 'W' and resid 85 through 91 Proline residue: W 89 - end of helix Processing helix chain 'W' and resid 94 through 102 Processing helix chain 'W' and resid 119 through 131 Processing helix chain 'W' and resid 163 through 170 Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.642A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 76 removed outlier: 3.601A pdb=" N ILE I 46 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Proline residue: I 47 - end of helix removed outlier: 4.322A pdb=" N ARG I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL I 56 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET I 57 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP I 61 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA I 62 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE I 63 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Proline residue: I 64 - end of helix removed outlier: 3.768A pdb=" N VAL I 68 " --> pdb=" O MET I 65 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU I 72 " --> pdb=" O GLY I 69 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR I 73 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE I 76 " --> pdb=" O TYR I 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.831A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 76 removed outlier: 3.761A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J 62 " --> pdb=" O GLY J 58 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.782A pdb=" N LEU L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR L 10 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 13 " --> pdb=" O TYR L 10 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL L 15 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET L 17 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY L 18 " --> pdb=" O VAL L 15 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU L 19 " --> pdb=" O MET L 16 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA L 20 " --> pdb=" O MET L 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE L 22 " --> pdb=" O LEU L 19 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA L 24 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA L 25 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE L 26 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY L 27 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE L 28 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE L 30 " --> pdb=" O GLY L 27 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY L 32 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY L 33 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS L 34 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU L 36 " --> pdb=" O GLY L 33 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU L 37 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA L 39 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 76 removed outlier: 3.504A pdb=" N ILE L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Proline residue: L 47 - end of helix removed outlier: 4.257A pdb=" N ARG L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE L 54 " --> pdb=" O THR L 51 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY L 58 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 60 " --> pdb=" O MET L 57 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE L 63 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Proline residue: L 64 - end of helix removed outlier: 4.158A pdb=" N VAL L 68 " --> pdb=" O MET L 65 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU L 70 " --> pdb=" O ALA L 67 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY L 71 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU L 72 " --> pdb=" O GLY L 69 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL L 74 " --> pdb=" O GLY L 71 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET L 75 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.505A pdb=" N LEU M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 76 Proline residue: M 47 - end of helix removed outlier: 4.201A pdb=" N ARG M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR M 51 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE M 53 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE M 54 " --> pdb=" O THR M 51 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET M 57 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY M 58 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL M 60 " --> pdb=" O MET M 57 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP M 61 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE M 63 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Proline residue: M 64 - end of helix removed outlier: 3.641A pdb=" N ALA M 67 " --> pdb=" O PRO M 64 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL M 68 " --> pdb=" O MET M 65 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU M 72 " --> pdb=" O GLY M 69 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE M 76 " --> pdb=" O TYR M 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 5.022A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 76 removed outlier: 3.637A pdb=" N ILE N 46 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Proline residue: N 47 - end of helix removed outlier: 4.128A pdb=" N ARG N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET N 57 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY N 58 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP N 61 " --> pdb=" O GLY N 58 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE N 63 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Proline residue: N 64 - end of helix removed outlier: 3.870A pdb=" N ALA N 67 " --> pdb=" O PRO N 64 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL N 68 " --> pdb=" O MET N 65 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY N 71 " --> pdb=" O VAL N 68 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU N 72 " --> pdb=" O GLY N 69 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL N 74 " --> pdb=" O GLY N 71 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE N 76 " --> pdb=" O TYR N 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 41 removed outlier: 3.695A pdb=" N ALA O 12 " --> pdb=" O LEU O 9 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA O 13 " --> pdb=" O TYR O 10 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL O 15 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET O 16 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET O 17 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY O 18 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU O 19 " --> pdb=" O MET O 16 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA O 20 " --> pdb=" O MET O 17 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY O 23 " --> pdb=" O ALA O 20 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA O 24 " --> pdb=" O ALA O 21 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA O 25 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE O 26 " --> pdb=" O GLY O 23 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY O 27 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE O 28 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE O 30 " --> pdb=" O GLY O 27 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU O 31 " --> pdb=" O ILE O 28 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY O 32 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY O 33 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS O 34 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU O 37 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA O 40 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG O 41 " --> pdb=" O GLY O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 76 removed outlier: 3.796A pdb=" N ILE O 46 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Proline residue: O 47 - end of helix removed outlier: 3.962A pdb=" N ARG O 50 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN O 52 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE O 53 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL O 56 " --> pdb=" O PHE O 53 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET O 57 " --> pdb=" O PHE O 54 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP O 61 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE O 63 " --> pdb=" O VAL O 60 " (cutoff:3.500A) Proline residue: O 64 - end of helix removed outlier: 3.506A pdb=" N ALA O 67 " --> pdb=" O PRO O 64 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL O 68 " --> pdb=" O MET O 65 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU O 70 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY O 71 " --> pdb=" O VAL O 68 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU O 72 " --> pdb=" O GLY O 69 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL O 74 " --> pdb=" O GLY O 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET O 75 " --> pdb=" O LEU O 72 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE O 76 " --> pdb=" O TYR O 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 41 removed outlier: 3.978A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 76 removed outlier: 3.978A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.744A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.576A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 76 Proline residue: Q 47 - end of helix removed outlier: 4.315A pdb=" N ARG Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE Q 54 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET Q 57 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE Q 63 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.778A pdb=" N ALA Q 67 " --> pdb=" O PRO Q 64 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL Q 68 " --> pdb=" O MET Q 65 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY Q 69 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU Q 70 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU Q 72 " --> pdb=" O GLY Q 69 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET Q 75 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE Q 76 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.564A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 76 Proline residue: R 47 - end of helix removed outlier: 3.894A pdb=" N ARG R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL R 56 " --> pdb=" O PHE R 53 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET R 57 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY R 58 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE R 63 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Proline residue: R 64 - end of helix removed outlier: 3.754A pdb=" N ALA R 67 " --> pdb=" O PRO R 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL R 68 " --> pdb=" O MET R 65 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 70 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY R 71 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU R 72 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL R 74 " --> pdb=" O GLY R 71 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET R 75 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 41 removed outlier: 4.565A pdb=" N TYR S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA S 12 " --> pdb=" O LEU S 9 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA S 13 " --> pdb=" O TYR S 10 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA S 14 " --> pdb=" O MET S 11 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL S 15 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET S 17 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY S 18 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU S 19 " --> pdb=" O MET S 16 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA S 20 " --> pdb=" O MET S 17 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE S 22 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY S 23 " --> pdb=" O ALA S 20 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA S 24 " --> pdb=" O ALA S 21 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA S 25 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE S 26 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY S 27 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE S 28 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE S 30 " --> pdb=" O GLY S 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU S 31 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY S 32 " --> pdb=" O GLY S 29 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY S 33 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS S 34 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU S 37 " --> pdb=" O LYS S 34 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA S 39 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 60 Proline residue: S 47 - end of helix removed outlier: 3.560A pdb=" N ARG S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE S 54 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE S 55 " --> pdb=" O GLN S 52 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET S 57 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY S 58 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 77 Processing helix chain 'X' and resid 5 through 23 removed outlier: 3.559A pdb=" N GLY X 9 " --> pdb=" O THR X 6 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN X 10 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE X 14 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU X 19 " --> pdb=" O LEU X 16 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE X 20 " --> pdb=" O PHE X 17 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS X 21 " --> pdb=" O VAL X 18 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS X 23 " --> pdb=" O PHE X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 135 removed outlier: 3.507A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 155 Processing helix chain 'Y' and resid 3 through 23 Processing helix chain 'Y' and resid 25 through 138 removed outlier: 4.390A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET Y 30 " --> pdb=" O TRP Y 26 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE Y 109 " --> pdb=" O ALA Y 105 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS Y 114 " --> pdb=" O GLU Y 110 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Y 120 " --> pdb=" O ALA Y 116 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 155 removed outlier: 3.761A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 16 Processing helix chain 'a' and resid 43 through 64 Processing helix chain 'a' and resid 76 through 93 removed outlier: 3.534A pdb=" N VAL a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 99 through 120 Proline residue: a 103 - end of helix removed outlier: 3.713A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU a 120 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 132 Processing helix chain 'a' and resid 143 through 145 No H-bonds generated for 'chain 'a' and resid 143 through 145' Processing helix chain 'a' and resid 147 through 180 removed outlier: 3.634A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 228 Proline residue: a 190 - end of helix removed outlier: 4.230A pdb=" N LEU a 193 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU a 196 " --> pdb=" O LEU a 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY a 197 " --> pdb=" O ILE a 194 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL a 198 " --> pdb=" O LEU a 195 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER a 199 " --> pdb=" O GLU a 196 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER a 202 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.817A pdb=" N GLY a 208 " --> pdb=" O VAL a 205 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU a 209 " --> pdb=" O SER a 206 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG a 210 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE a 212 " --> pdb=" O LEU a 209 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY a 213 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN a 214 " --> pdb=" O LEU a 211 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR a 216 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA a 217 " --> pdb=" O ASN a 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY a 218 " --> pdb=" O MET a 215 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU a 219 " --> pdb=" O TYR a 216 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU a 220 " --> pdb=" O ALA a 217 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE a 225 " --> pdb=" O PHE a 222 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA a 226 " --> pdb=" O ILE a 223 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU a 228 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 268 removed outlier: 4.629A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.585A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER a 268 " --> pdb=" O LEU a 264 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.782A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.382A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL A 224 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER A 323 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE A 258 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 325 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR A 260 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 327 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.600A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.315A pdb=" N ASN B 27 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.320A pdb=" N VAL B 108 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 223 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL B 224 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 198 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER B 323 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE B 258 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR B 325 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR B 260 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.658A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.322A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.386A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL C 224 " --> pdb=" O ALA C 193 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER C 323 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE C 258 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR C 325 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TYR C 260 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU C 327 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 351 through 355 Processing sheet with id= M, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.460A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= O, first strand: chain 'D' and resid 317 through 320 removed outlier: 8.074A pdb=" N VAL D 145 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER D 292 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU D 147 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN D 294 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY D 149 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL D 296 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 67 through 69 removed outlier: 6.501A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE E 54 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL E 42 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= R, first strand: chain 'E' and resid 317 through 320 removed outlier: 7.910A pdb=" N VAL E 145 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER E 292 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU E 147 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLN E 294 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY E 149 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL E 296 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR E 297 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 4 through 9 removed outlier: 6.576A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.505A pdb=" N VAL F 79 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 317 through 319 removed outlier: 8.682A pdb=" N VAL F 145 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER F 292 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU F 147 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN F 294 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR F 173 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N PHE F 240 " --> pdb=" O TYR F 173 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL F 175 " --> pdb=" O PHE F 240 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 181 through 188 removed outlier: 6.625A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN G 111 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N TYR G 77 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP G 113 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 134 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 42 through 45 removed outlier: 4.212A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ALA H 80 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL H 9 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR H 4 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER H 10 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN H 14 " --> pdb=" O SER H 10 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 32 through 34 removed outlier: 3.785A pdb=" N ILE H 23 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N THR H 82 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'W' and resid 135 through 138 Processing sheet with id= Z, first strand: chain 'a' and resid 20 through 22 1858 hydrogen bonds defined for protein. 4881 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: 12.18 Time building geometry restraints manager: 15.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6354 1.31 - 1.44: 8780 1.44 - 1.56: 21971 1.56 - 1.69: 30 1.69 - 1.82: 358 Bond restraints: 37493 Sorted by residual: bond pdb=" C VAL a 50 " pdb=" N VAL a 51 " ideal model delta sigma weight residual 1.334 1.426 -0.092 1.26e-02 6.30e+03 5.31e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C4 ATP D 502 " pdb=" C5 ATP D 502 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.55e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.40e+01 ... (remaining 37488 not shown) Histogram of bond angle deviations from ideal: 96.89 - 104.74: 736 104.74 - 112.59: 18321 112.59 - 120.44: 17707 120.44 - 128.29: 13783 128.29 - 136.14: 203 Bond angle restraints: 50750 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.74 22.13 1.00e+00 1.00e+00 4.90e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 119.86 20.01 1.00e+00 1.00e+00 4.00e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 120.75 19.12 1.00e+00 1.00e+00 3.66e+02 angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 122.82 17.05 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 121.97 14.86 1.00e+00 1.00e+00 2.21e+02 ... (remaining 50745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 22333 35.39 - 70.78: 407 70.78 - 106.16: 54 106.16 - 141.55: 3 141.55 - 176.94: 2 Dihedral angle restraints: 22799 sinusoidal: 9027 harmonic: 13772 Sorted by residual: dihedral pdb=" C ARG C 365 " pdb=" N ARG C 365 " pdb=" CA ARG C 365 " pdb=" CB ARG C 365 " ideal model delta harmonic sigma weight residual -122.60 -152.93 30.33 0 2.50e+00 1.60e-01 1.47e+02 dihedral pdb=" N ARG C 365 " pdb=" C ARG C 365 " pdb=" CA ARG C 365 " pdb=" CB ARG C 365 " ideal model delta harmonic sigma weight residual 122.80 152.43 -29.63 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 123.06 176.94 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 22796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 5880 0.260 - 0.520: 35 0.520 - 0.780: 0 0.780 - 1.040: 0 1.040 - 1.300: 1 Chirality restraints: 5916 Sorted by residual: chirality pdb=" CA ARG C 365 " pdb=" N ARG C 365 " pdb=" C ARG C 365 " pdb=" CB ARG C 365 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.23e+01 chirality pdb=" CB ILE Q 63 " pdb=" CA ILE Q 63 " pdb=" CG1 ILE Q 63 " pdb=" CG2 ILE Q 63 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CB ILE E 330 " pdb=" CA ILE E 330 " pdb=" CG1 ILE E 330 " pdb=" CG2 ILE E 330 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 5913 not shown) Planarity restraints: 6545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG X 36 " -0.132 9.50e-02 1.11e+02 7.53e-02 2.91e+01 pdb=" NE ARG X 36 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG X 36 " -0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG X 36 " 0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG X 36 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 41 " -0.277 9.50e-02 1.11e+02 1.28e-01 2.24e+01 pdb=" NE ARG R 41 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG R 41 " 0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG R 41 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG R 41 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 281 " -0.124 9.50e-02 1.11e+02 6.89e-02 2.24e+01 pdb=" NE ARG D 281 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 281 " -0.077 2.00e-02 2.50e+03 pdb=" NH1 ARG D 281 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG D 281 " 0.021 2.00e-02 2.50e+03 ... (remaining 6542 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 35 2.45 - 3.06: 24490 3.06 - 3.67: 55109 3.67 - 4.29: 84909 4.29 - 4.90: 140702 Nonbonded interactions: 305245 Sorted by model distance: nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.833 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.854 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.863 2.170 nonbonded pdb="MG MG D 501 " pdb=" O1G ATP D 502 " model vdw 1.875 2.170 nonbonded pdb="MG MG D 501 " pdb=" O1B ATP D 502 " model vdw 1.899 2.170 ... (remaining 305240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.240 Check model and map are aligned: 0.490 Set scattering table: 0.330 Process input model: 91.920 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.010 0.103 37493 Z= 0.665 Angle : 1.264 22.133 50750 Z= 0.822 Chirality : 0.073 1.300 5916 Planarity : 0.008 0.128 6545 Dihedral : 14.819 176.941 13989 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 0.65 % Allowed : 5.19 % Favored : 94.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.11), residues: 4803 helix: -1.28 (0.08), residues: 2616 sheet: 0.09 (0.21), residues: 547 loop : -0.77 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP a 111 HIS 0.021 0.003 HIS D 191 PHE 0.052 0.004 PHE L 54 TYR 0.044 0.007 TYR F 26 ARG 0.090 0.011 ARG X 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 395 time to evaluate : 4.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8423 (mtt) cc_final: 0.8124 (mtt) REVERT: A 236 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8746 (p90) REVERT: C 386 MET cc_start: 0.9167 (mmm) cc_final: 0.8588 (mmm) REVERT: D 226 MET cc_start: 0.8994 (mtt) cc_final: 0.8767 (mtt) REVERT: E 88 MET cc_start: 0.8826 (mtm) cc_final: 0.8553 (mtp) REVERT: F 261 MET cc_start: 0.8813 (mtt) cc_final: 0.8608 (ttt) REVERT: F 379 MET cc_start: 0.8221 (tpp) cc_final: 0.7812 (tpp) REVERT: G 116 MET cc_start: 0.8867 (mpp) cc_final: 0.8578 (mmt) REVERT: G 215 LEU cc_start: 0.9524 (tp) cc_final: 0.9317 (pp) REVERT: G 224 GLU cc_start: 0.8692 (tt0) cc_final: 0.8395 (pt0) REVERT: G 243 MET cc_start: 0.8694 (ttp) cc_final: 0.8373 (ttp) REVERT: H 13 GLN cc_start: 0.6760 (pt0) cc_final: 0.6491 (pp30) REVERT: H 40 PRO cc_start: 0.6101 (Cg_exo) cc_final: 0.5896 (Cg_exo) REVERT: H 63 TYR cc_start: 0.5439 (t80) cc_final: 0.5132 (t80) REVERT: H 127 GLN cc_start: 0.8912 (mt0) cc_final: 0.8688 (tt0) REVERT: W 30 MET cc_start: 0.8977 (ttp) cc_final: 0.8553 (ttm) REVERT: L 17 MET cc_start: 0.3167 (mtm) cc_final: 0.2006 (ttt) REVERT: L 59 LEU cc_start: 0.2125 (OUTLIER) cc_final: 0.1899 (mt) REVERT: N 17 MET cc_start: 0.2425 (mtp) cc_final: 0.1289 (tpt) REVERT: O 11 MET cc_start: -0.5304 (tpt) cc_final: -0.5511 (tpt) REVERT: O 17 MET cc_start: -0.1743 (ttm) cc_final: -0.2144 (mmm) REVERT: P 6 MET cc_start: 0.3592 (mmt) cc_final: 0.3057 (ppp) REVERT: P 17 MET cc_start: -0.0122 (mtm) cc_final: -0.1372 (mtm) REVERT: Q 28 ILE cc_start: 0.4329 (mt) cc_final: 0.3822 (mt) REVERT: Q 37 GLU cc_start: 0.8714 (tp30) cc_final: 0.8439 (pt0) REVERT: Q 57 MET cc_start: 0.5521 (tmm) cc_final: 0.4395 (ptm) REVERT: Q 65 MET cc_start: 0.5785 (mtt) cc_final: 0.5360 (tpp) REVERT: X 73 GLN cc_start: 0.8968 (mp-120) cc_final: 0.8732 (mm-40) REVERT: X 83 ARG cc_start: 0.8739 (ttp-110) cc_final: 0.8503 (ttp80) REVERT: X 123 GLN cc_start: 0.9360 (mm110) cc_final: 0.9077 (mm110) REVERT: X 127 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8568 (mp) REVERT: Y 117 ARG cc_start: 0.9082 (mtp180) cc_final: 0.8863 (mtm-85) REVERT: a 6 MET cc_start: -0.0629 (mmp) cc_final: -0.0881 (mtt) REVERT: a 68 THR cc_start: 0.5346 (p) cc_final: 0.4944 (t) REVERT: a 92 ASP cc_start: 0.7891 (m-30) cc_final: 0.7456 (t0) outliers start: 25 outliers final: 4 residues processed: 417 average time/residue: 0.5581 time to fit residues: 361.7162 Evaluate side-chains 270 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 263 time to evaluate : 4.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain X residue 127 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 20.0000 chunk 358 optimal weight: 0.0980 chunk 198 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 370 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 429 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 147 GLN A 186 GLN A 484 GLN B 58 ASN C 147 GLN C 344 ASN C 358 ASN D 35 ASN E 210 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN E 368 GLN F 19 GLN F 365 GLN F 368 GLN G 126 ASN G 135 GLN W 71 ASN W 73 GLN W 82 ASN I 52 GLN M 42 GLN O 3 ASN R 3 ASN R 5 ASN S 5 ASN ** X 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 GLN a 17 ASN a 20 GLN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37493 Z= 0.200 Angle : 0.621 8.716 50750 Z= 0.325 Chirality : 0.043 0.372 5916 Planarity : 0.004 0.053 6545 Dihedral : 8.429 164.546 5376 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.48 % Favored : 98.50 % Rotamer: Outliers : 1.30 % Allowed : 7.54 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.12), residues: 4803 helix: 0.55 (0.10), residues: 2605 sheet: 0.53 (0.21), residues: 527 loop : -0.24 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 105 HIS 0.011 0.001 HIS a 14 PHE 0.018 0.002 PHE F 189 TYR 0.022 0.001 TYR B 236 ARG 0.006 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 292 time to evaluate : 4.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8443 (mtt) cc_final: 0.8198 (mtt) REVERT: A 415 ASP cc_start: 0.7986 (t0) cc_final: 0.7074 (t0) REVERT: A 488 GLN cc_start: 0.8675 (mm110) cc_final: 0.8381 (mm110) REVERT: C 386 MET cc_start: 0.9174 (mmm) cc_final: 0.8918 (mmm) REVERT: D 209 MET cc_start: 0.9119 (ptp) cc_final: 0.8662 (ptp) REVERT: F 261 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8483 (ttt) REVERT: F 379 MET cc_start: 0.8340 (tpp) cc_final: 0.8091 (tpp) REVERT: G 116 MET cc_start: 0.8588 (mpp) cc_final: 0.8350 (mmt) REVERT: G 151 PRO cc_start: 0.9302 (Cg_exo) cc_final: 0.9022 (Cg_endo) REVERT: H 7 ASP cc_start: 0.5609 (t0) cc_final: 0.4858 (p0) REVERT: H 52 ILE cc_start: 0.4457 (OUTLIER) cc_final: 0.4199 (mt) REVERT: W 30 MET cc_start: 0.8396 (ttp) cc_final: 0.8181 (ttp) REVERT: W 67 GLN cc_start: 0.7047 (mm110) cc_final: 0.6843 (mm-40) REVERT: W 124 ILE cc_start: 0.9179 (tt) cc_final: 0.8971 (pt) REVERT: W 147 MET cc_start: 0.8307 (mmt) cc_final: 0.7857 (mmp) REVERT: W 157 MET cc_start: 0.7413 (mpp) cc_final: 0.7158 (mpp) REVERT: J 11 MET cc_start: 0.1208 (mmm) cc_final: 0.0606 (ppp) REVERT: L 17 MET cc_start: 0.2274 (mtm) cc_final: 0.1552 (ttm) REVERT: N 16 MET cc_start: -0.0389 (mmm) cc_final: -0.0859 (mmm) REVERT: O 6 MET cc_start: -0.1329 (ptm) cc_final: -0.1537 (ptp) REVERT: O 17 MET cc_start: -0.1878 (ttm) cc_final: -0.2225 (mmt) REVERT: P 6 MET cc_start: 0.4332 (mmt) cc_final: 0.3726 (ppp) REVERT: Q 57 MET cc_start: 0.5613 (tmm) cc_final: 0.4608 (ptm) REVERT: Q 65 MET cc_start: 0.6092 (mtt) cc_final: 0.5453 (tpp) REVERT: R 17 MET cc_start: 0.1307 (mtp) cc_final: 0.0966 (mtm) REVERT: X 73 GLN cc_start: 0.8884 (mp-120) cc_final: 0.8640 (mm-40) REVERT: X 83 ARG cc_start: 0.8790 (ttp-110) cc_final: 0.8590 (ttp80) REVERT: X 85 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8601 (mt0) REVERT: X 123 GLN cc_start: 0.9287 (mm110) cc_final: 0.8935 (mm110) REVERT: Y 1 MET cc_start: 0.1022 (ttp) cc_final: -0.1126 (mmm) REVERT: Y 78 GLN cc_start: 0.7601 (tp40) cc_final: 0.7172 (mm-40) REVERT: Y 98 ARG cc_start: 0.8890 (tpt170) cc_final: 0.8636 (tpp80) REVERT: a 6 MET cc_start: -0.0165 (mmp) cc_final: -0.0505 (mtt) REVERT: a 92 ASP cc_start: 0.7333 (m-30) cc_final: 0.7060 (t70) REVERT: a 168 MET cc_start: 0.6073 (mmp) cc_final: 0.5822 (ttm) outliers start: 50 outliers final: 15 residues processed: 330 average time/residue: 0.4883 time to fit residues: 266.7952 Evaluate side-chains 269 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 252 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Y residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 357 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 430 optimal weight: 20.0000 chunk 464 optimal weight: 9.9990 chunk 383 optimal weight: 9.9990 chunk 426 optimal weight: 6.9990 chunk 146 optimal weight: 0.0170 chunk 345 optimal weight: 8.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN F 208 GLN G 111 GLN G 157 GLN X 64 GLN ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 32 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 37493 Z= 0.356 Angle : 0.614 10.537 50750 Z= 0.317 Chirality : 0.044 0.272 5916 Planarity : 0.004 0.050 6545 Dihedral : 7.959 143.574 5368 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.43 % Allowed : 8.82 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.12), residues: 4803 helix: 1.00 (0.10), residues: 2617 sheet: 0.50 (0.21), residues: 537 loop : -0.21 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 105 HIS 0.007 0.001 HIS D 191 PHE 0.023 0.001 PHE F 189 TYR 0.029 0.002 TYR a 263 ARG 0.009 0.001 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 261 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8613 (mtt) cc_final: 0.8165 (mtt) REVERT: A 236 TYR cc_start: 0.9427 (OUTLIER) cc_final: 0.8886 (p90) REVERT: B 386 MET cc_start: 0.9456 (mmt) cc_final: 0.9234 (mmt) REVERT: C 365 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7000 (mmt90) REVERT: C 386 MET cc_start: 0.9141 (mmm) cc_final: 0.8875 (mmm) REVERT: C 409 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7231 (p90) REVERT: E 193 MET cc_start: 0.8908 (mmp) cc_final: 0.8677 (mmp) REVERT: F 379 MET cc_start: 0.8426 (tpp) cc_final: 0.8177 (tpp) REVERT: G 116 MET cc_start: 0.8597 (mpp) cc_final: 0.8386 (mmt) REVERT: H 49 MET cc_start: 0.4498 (ttp) cc_final: 0.4270 (ttp) REVERT: W 30 MET cc_start: 0.8526 (ttp) cc_final: 0.7804 (ttm) REVERT: W 124 ILE cc_start: 0.9154 (tt) cc_final: 0.8936 (pt) REVERT: W 157 MET cc_start: 0.7480 (mpp) cc_final: 0.7244 (mpp) REVERT: J 11 MET cc_start: 0.0968 (mmm) cc_final: 0.0324 (ppp) REVERT: L 17 MET cc_start: 0.1979 (mtm) cc_final: 0.1296 (ttm) REVERT: N 35 PHE cc_start: 0.5784 (t80) cc_final: 0.5387 (t80) REVERT: P 6 MET cc_start: 0.4196 (mmt) cc_final: 0.3709 (ppp) REVERT: Q 57 MET cc_start: 0.5317 (tmm) cc_final: 0.4467 (ptm) REVERT: Q 65 MET cc_start: 0.5985 (mtt) cc_final: 0.5597 (mmm) REVERT: R 17 MET cc_start: 0.1405 (mtp) cc_final: 0.0998 (mtm) REVERT: X 73 GLN cc_start: 0.8828 (mp-120) cc_final: 0.8585 (mm-40) REVERT: Y 98 ARG cc_start: 0.8929 (tpt170) cc_final: 0.8691 (tpp80) outliers start: 55 outliers final: 29 residues processed: 303 average time/residue: 0.4736 time to fit residues: 240.6131 Evaluate side-chains 280 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 248 time to evaluate : 4.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 19 GLN Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 104 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 8.9990 chunk 323 optimal weight: 40.0000 chunk 223 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 431 optimal weight: 40.0000 chunk 457 optimal weight: 30.0000 chunk 225 optimal weight: 8.9990 chunk 409 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN E 210 ASN F 353 HIS ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 37493 Z= 0.295 Angle : 0.562 8.628 50750 Z= 0.289 Chirality : 0.042 0.233 5916 Planarity : 0.004 0.046 6545 Dihedral : 7.593 134.961 5368 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.72 % Allowed : 9.44 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.12), residues: 4803 helix: 1.24 (0.10), residues: 2612 sheet: 0.43 (0.21), residues: 543 loop : -0.28 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 231 HIS 0.005 0.001 HIS a 14 PHE 0.018 0.001 PHE S 35 TYR 0.026 0.001 TYR a 263 ARG 0.005 0.000 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 249 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8646 (mtt) cc_final: 0.8233 (mtt) REVERT: C 386 MET cc_start: 0.9109 (mmm) cc_final: 0.8860 (mmm) REVERT: C 409 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7224 (p90) REVERT: E 210 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: F 379 MET cc_start: 0.8467 (tpp) cc_final: 0.8133 (tpp) REVERT: G 31 MET cc_start: 0.8976 (ttp) cc_final: 0.8702 (ttp) REVERT: G 116 MET cc_start: 0.8443 (mpp) cc_final: 0.8197 (mmt) REVERT: W 30 MET cc_start: 0.8793 (ttp) cc_final: 0.8097 (ttm) REVERT: W 147 MET cc_start: 0.8292 (mmt) cc_final: 0.7987 (mmp) REVERT: J 11 MET cc_start: 0.0899 (mmm) cc_final: 0.0221 (ppp) REVERT: L 17 MET cc_start: 0.1837 (mtm) cc_final: 0.1141 (ttm) REVERT: M 75 MET cc_start: 0.2134 (tmm) cc_final: 0.1787 (ttt) REVERT: N 35 PHE cc_start: 0.5775 (t80) cc_final: 0.5383 (t80) REVERT: P 6 MET cc_start: 0.4203 (mmt) cc_final: 0.3754 (ppp) REVERT: Q 57 MET cc_start: 0.5219 (tmm) cc_final: 0.4334 (ptm) REVERT: Q 65 MET cc_start: 0.5970 (mtt) cc_final: 0.5489 (mmm) REVERT: R 65 MET cc_start: 0.3878 (mmm) cc_final: 0.2996 (tpt) REVERT: X 73 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8539 (mm-40) REVERT: Y 98 ARG cc_start: 0.8962 (tpt170) cc_final: 0.8749 (tpp80) REVERT: Y 106 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8298 (tm-30) outliers start: 66 outliers final: 34 residues processed: 301 average time/residue: 0.4633 time to fit residues: 235.4731 Evaluate side-chains 275 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 104 GLN Chi-restraints excluded: chain a residue 79 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 340 optimal weight: 0.0370 chunk 188 optimal weight: 0.8980 chunk 390 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 410 optimal weight: 5.9990 chunk 115 optimal weight: 0.3980 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 210 ASN F 19 GLN ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37493 Z= 0.168 Angle : 0.527 9.600 50750 Z= 0.268 Chirality : 0.040 0.226 5916 Planarity : 0.004 0.044 6545 Dihedral : 7.149 128.865 5368 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.28 % Allowed : 10.57 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.12), residues: 4803 helix: 1.40 (0.10), residues: 2615 sheet: 0.58 (0.21), residues: 540 loop : -0.19 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 26 HIS 0.004 0.001 HIS a 14 PHE 0.018 0.001 PHE S 35 TYR 0.026 0.001 TYR a 263 ARG 0.005 0.000 ARG H 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 4.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8623 (mtt) cc_final: 0.8340 (mtt) REVERT: C 365 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6721 (mmt90) REVERT: C 386 MET cc_start: 0.9056 (mmm) cc_final: 0.8815 (mmm) REVERT: C 409 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7136 (p90) REVERT: E 210 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8284 (m-40) REVERT: F 379 MET cc_start: 0.8451 (tpp) cc_final: 0.7997 (tpp) REVERT: G 116 MET cc_start: 0.8338 (mpp) cc_final: 0.8111 (mmt) REVERT: G 243 MET cc_start: 0.8698 (ttp) cc_final: 0.8357 (ttp) REVERT: H 7 ASP cc_start: 0.5604 (t70) cc_final: 0.5008 (p0) REVERT: H 13 GLN cc_start: 0.5496 (pm20) cc_final: 0.5257 (pm20) REVERT: W 147 MET cc_start: 0.8314 (mmt) cc_final: 0.7997 (mmp) REVERT: J 11 MET cc_start: 0.0976 (mmm) cc_final: 0.0294 (tmm) REVERT: L 17 MET cc_start: 0.1790 (mtm) cc_final: 0.0714 (ttm) REVERT: M 75 MET cc_start: 0.2201 (tmm) cc_final: 0.1932 (ttt) REVERT: N 35 PHE cc_start: 0.5706 (t80) cc_final: 0.5317 (t80) REVERT: N 65 MET cc_start: 0.1608 (mmt) cc_final: 0.0280 (tpt) REVERT: P 6 MET cc_start: 0.3989 (mmt) cc_final: 0.3522 (ppp) REVERT: Q 57 MET cc_start: 0.4826 (tmm) cc_final: 0.3972 (ptm) REVERT: Q 65 MET cc_start: 0.5955 (mtt) cc_final: 0.5424 (mmm) REVERT: R 65 MET cc_start: 0.4016 (mmm) cc_final: 0.3188 (tpt) REVERT: X 73 GLN cc_start: 0.8815 (mp-120) cc_final: 0.8524 (mm-40) REVERT: Y 3 LEU cc_start: -0.2942 (OUTLIER) cc_final: -0.3190 (tp) REVERT: Y 22 MET cc_start: -0.1877 (tpp) cc_final: -0.2406 (tmm) REVERT: Y 121 ARG cc_start: 0.8695 (tmm-80) cc_final: 0.8484 (tmm-80) outliers start: 49 outliers final: 28 residues processed: 291 average time/residue: 0.4658 time to fit residues: 228.7111 Evaluate side-chains 276 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 244 time to evaluate : 4.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 104 GLN Chi-restraints excluded: chain a residue 79 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 5.9990 chunk 411 optimal weight: 50.0000 chunk 90 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 457 optimal weight: 50.0000 chunk 379 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 210 ASN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37493 Z= 0.268 Angle : 0.552 10.051 50750 Z= 0.279 Chirality : 0.041 0.210 5916 Planarity : 0.004 0.045 6545 Dihedral : 7.020 122.273 5368 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.59 % Allowed : 11.30 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.12), residues: 4803 helix: 1.47 (0.10), residues: 2598 sheet: 0.57 (0.21), residues: 542 loop : -0.22 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 231 HIS 0.004 0.001 HIS D 191 PHE 0.018 0.001 PHE S 35 TYR 0.024 0.001 TYR a 263 ARG 0.007 0.000 ARG X 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 246 time to evaluate : 5.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8649 (mtt) cc_final: 0.8229 (mtt) REVERT: C 365 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6814 (mmt90) REVERT: C 386 MET cc_start: 0.9073 (mmm) cc_final: 0.8843 (mmm) REVERT: C 409 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7141 (p90) REVERT: F 379 MET cc_start: 0.8477 (tpp) cc_final: 0.8015 (tpp) REVERT: G 31 MET cc_start: 0.8902 (ttp) cc_final: 0.8661 (ttp) REVERT: G 116 MET cc_start: 0.8381 (mpp) cc_final: 0.8160 (mmt) REVERT: H 7 ASP cc_start: 0.5782 (t70) cc_final: 0.5263 (p0) REVERT: H 51 ARG cc_start: 0.6487 (mtm-85) cc_final: 0.6232 (mtm-85) REVERT: W 147 MET cc_start: 0.8336 (mmt) cc_final: 0.8004 (mmp) REVERT: J 11 MET cc_start: 0.1064 (mmm) cc_final: 0.0381 (tmm) REVERT: L 17 MET cc_start: 0.1515 (mtm) cc_final: 0.0687 (ttm) REVERT: M 75 MET cc_start: 0.2167 (tmm) cc_final: 0.1946 (ttt) REVERT: N 35 PHE cc_start: 0.5745 (t80) cc_final: 0.5439 (t80) REVERT: N 65 MET cc_start: 0.1598 (mmt) cc_final: 0.0330 (tpt) REVERT: P 6 MET cc_start: 0.4008 (mmt) cc_final: 0.3533 (ppp) REVERT: Q 57 MET cc_start: 0.4795 (tmm) cc_final: 0.3962 (ptm) REVERT: Q 65 MET cc_start: 0.5985 (mtt) cc_final: 0.5397 (mmm) REVERT: R 65 MET cc_start: 0.3973 (mmm) cc_final: 0.3194 (tpt) REVERT: X 73 GLN cc_start: 0.8778 (mp-120) cc_final: 0.8510 (mm-40) REVERT: X 85 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8576 (mp10) REVERT: X 115 ARG cc_start: 0.8890 (mtp-110) cc_final: 0.8674 (mtp-110) REVERT: X 123 GLN cc_start: 0.9072 (mm110) cc_final: 0.8701 (mm110) REVERT: Y 3 LEU cc_start: -0.2924 (OUTLIER) cc_final: -0.3163 (tp) REVERT: Y 121 ARG cc_start: 0.8766 (tmm-80) cc_final: 0.8515 (tmm-80) outliers start: 61 outliers final: 39 residues processed: 294 average time/residue: 0.4615 time to fit residues: 228.9205 Evaluate side-chains 284 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 242 time to evaluate : 4.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Y residue 104 GLN Chi-restraints excluded: chain Y residue 151 LYS Chi-restraints excluded: chain a residue 46 MET Chi-restraints excluded: chain a residue 79 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 260 optimal weight: 9.9990 chunk 334 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 385 optimal weight: 50.0000 chunk 255 optimal weight: 8.9990 chunk 455 optimal weight: 10.0000 chunk 285 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 210 ASN H 58 HIS I 42 GLN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 37493 Z= 0.292 Angle : 0.563 11.038 50750 Z= 0.284 Chirality : 0.041 0.201 5916 Planarity : 0.004 0.045 6545 Dihedral : 6.910 114.348 5366 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.28 % Allowed : 11.97 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.12), residues: 4803 helix: 1.53 (0.10), residues: 2586 sheet: 0.53 (0.21), residues: 534 loop : -0.30 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 231 HIS 0.005 0.001 HIS D 191 PHE 0.019 0.001 PHE S 35 TYR 0.019 0.001 TYR a 263 ARG 0.009 0.000 ARG X 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 251 time to evaluate : 4.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8666 (mtt) cc_final: 0.8262 (mtt) REVERT: B 1 MET cc_start: 0.6025 (tpp) cc_final: 0.5496 (ttt) REVERT: C 365 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.6811 (mmt90) REVERT: C 386 MET cc_start: 0.9064 (mmm) cc_final: 0.8839 (mmm) REVERT: C 409 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7044 (p90) REVERT: F 379 MET cc_start: 0.8504 (tpp) cc_final: 0.8060 (tpp) REVERT: G 31 MET cc_start: 0.8911 (ttp) cc_final: 0.8557 (ttp) REVERT: G 116 MET cc_start: 0.8375 (mpp) cc_final: 0.8157 (mmt) REVERT: H 7 ASP cc_start: 0.5818 (t70) cc_final: 0.5300 (p0) REVERT: H 51 ARG cc_start: 0.6504 (mtm-85) cc_final: 0.5901 (ttm-80) REVERT: W 147 MET cc_start: 0.8342 (mmt) cc_final: 0.8010 (mmp) REVERT: I 17 MET cc_start: 0.3611 (ppp) cc_final: 0.2879 (ttp) REVERT: J 11 MET cc_start: 0.0990 (mmm) cc_final: 0.0326 (tmm) REVERT: L 17 MET cc_start: 0.1167 (mtm) cc_final: 0.0679 (ttm) REVERT: M 75 MET cc_start: 0.2274 (tmm) cc_final: 0.2029 (ttt) REVERT: N 35 PHE cc_start: 0.5841 (t80) cc_final: 0.5539 (t80) REVERT: N 65 MET cc_start: 0.1498 (mmt) cc_final: 0.0157 (tpt) REVERT: P 6 MET cc_start: 0.3967 (mmt) cc_final: 0.3497 (ppp) REVERT: Q 57 MET cc_start: 0.4834 (tmm) cc_final: 0.4022 (ptm) REVERT: Q 65 MET cc_start: 0.6107 (mtt) cc_final: 0.5236 (tpp) REVERT: R 65 MET cc_start: 0.4047 (mmm) cc_final: 0.3293 (tpt) REVERT: X 73 GLN cc_start: 0.8769 (mp-120) cc_final: 0.8515 (mm-40) REVERT: X 85 GLN cc_start: 0.8925 (mm-40) cc_final: 0.8599 (mt0) REVERT: X 123 GLN cc_start: 0.9061 (mm110) cc_final: 0.8740 (mm-40) REVERT: Y 3 LEU cc_start: -0.2623 (OUTLIER) cc_final: -0.2860 (tp) REVERT: Y 22 MET cc_start: -0.1988 (tpp) cc_final: -0.2503 (tmm) REVERT: Y 121 ARG cc_start: 0.8805 (tmm-80) cc_final: 0.8540 (tmm-80) outliers start: 49 outliers final: 37 residues processed: 290 average time/residue: 0.4662 time to fit residues: 224.8003 Evaluate side-chains 283 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 243 time to evaluate : 4.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 104 GLN Chi-restraints excluded: chain a residue 46 MET Chi-restraints excluded: chain a residue 79 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 289 optimal weight: 0.0980 chunk 310 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 358 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 274 GLN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37493 Z= 0.196 Angle : 0.539 11.996 50750 Z= 0.271 Chirality : 0.040 0.209 5916 Planarity : 0.004 0.044 6545 Dihedral : 6.618 99.603 5366 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.10 % Allowed : 12.60 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.12), residues: 4803 helix: 1.58 (0.10), residues: 2585 sheet: 0.59 (0.21), residues: 531 loop : -0.26 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 513 HIS 0.003 0.001 HIS W 21 PHE 0.020 0.001 PHE S 35 TYR 0.019 0.001 TYR a 263 ARG 0.012 0.000 ARG X 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 248 time to evaluate : 4.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8658 (mtt) cc_final: 0.8247 (mtt) REVERT: C 365 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6762 (mmt90) REVERT: C 386 MET cc_start: 0.9031 (mmm) cc_final: 0.8827 (mmm) REVERT: C 409 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7031 (p90) REVERT: F 379 MET cc_start: 0.8438 (tpp) cc_final: 0.8030 (tpp) REVERT: G 116 MET cc_start: 0.8325 (mpp) cc_final: 0.8089 (mmt) REVERT: G 243 MET cc_start: 0.8656 (ttp) cc_final: 0.8311 (ttp) REVERT: H 7 ASP cc_start: 0.6053 (t70) cc_final: 0.5634 (p0) REVERT: H 51 ARG cc_start: 0.6599 (mtm-85) cc_final: 0.6164 (mmm-85) REVERT: W 147 MET cc_start: 0.8373 (mmt) cc_final: 0.8035 (mmp) REVERT: I 6 MET cc_start: 0.1853 (tmm) cc_final: 0.1587 (tmm) REVERT: I 16 MET cc_start: 0.5145 (ptm) cc_final: 0.4794 (ptm) REVERT: I 17 MET cc_start: 0.3763 (ppp) cc_final: 0.3307 (mtm) REVERT: I 75 MET cc_start: -0.3288 (ttt) cc_final: -0.3736 (ttm) REVERT: J 11 MET cc_start: 0.1055 (mmm) cc_final: 0.0404 (tmm) REVERT: L 17 MET cc_start: 0.1115 (mtm) cc_final: 0.0266 (ttm) REVERT: L 65 MET cc_start: 0.1818 (ptt) cc_final: -0.0397 (tpt) REVERT: M 75 MET cc_start: 0.2286 (tmm) cc_final: 0.1898 (ttt) REVERT: N 35 PHE cc_start: 0.5777 (t80) cc_final: 0.5478 (t80) REVERT: P 6 MET cc_start: 0.3852 (mmt) cc_final: 0.3409 (ppp) REVERT: P 16 MET cc_start: -0.5186 (ttt) cc_final: -0.5889 (tpt) REVERT: P 65 MET cc_start: -0.2922 (mmt) cc_final: -0.3247 (ptp) REVERT: Q 57 MET cc_start: 0.4552 (tmm) cc_final: 0.3736 (ptm) REVERT: Q 65 MET cc_start: 0.6113 (mtt) cc_final: 0.5632 (mmm) REVERT: R 65 MET cc_start: 0.3922 (mmm) cc_final: 0.3193 (tpt) REVERT: S 35 PHE cc_start: 0.5126 (t80) cc_final: 0.4590 (t80) REVERT: X 73 GLN cc_start: 0.8756 (mp-120) cc_final: 0.8489 (mm-40) REVERT: X 82 ARG cc_start: 0.9004 (mmm160) cc_final: 0.8764 (mmm160) REVERT: X 123 GLN cc_start: 0.8989 (mm110) cc_final: 0.8689 (mm-40) REVERT: Y 3 LEU cc_start: -0.2589 (OUTLIER) cc_final: -0.2853 (tp) REVERT: Y 22 MET cc_start: -0.1866 (tpp) cc_final: -0.2417 (tmm) REVERT: Y 98 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.8187 (tpp-160) REVERT: Y 121 ARG cc_start: 0.8756 (tmm-80) cc_final: 0.8511 (tmm-80) outliers start: 42 outliers final: 31 residues processed: 281 average time/residue: 0.4844 time to fit residues: 226.8366 Evaluate side-chains 277 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 44 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 104 GLN Chi-restraints excluded: chain a residue 79 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 10.0000 chunk 436 optimal weight: 8.9990 chunk 398 optimal weight: 30.0000 chunk 424 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 333 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 383 optimal weight: 30.0000 chunk 401 optimal weight: 0.9980 chunk 423 optimal weight: 7.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 361 GLN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37493 Z= 0.345 Angle : 0.594 12.308 50750 Z= 0.298 Chirality : 0.042 0.204 5916 Planarity : 0.004 0.045 6545 Dihedral : 6.736 98.376 5366 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.25 % Allowed : 12.52 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.12), residues: 4803 helix: 1.53 (0.10), residues: 2592 sheet: 0.48 (0.21), residues: 531 loop : -0.36 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 513 HIS 0.005 0.001 HIS D 191 PHE 0.019 0.001 PHE S 35 TYR 0.017 0.001 TYR a 263 ARG 0.013 0.000 ARG Y 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 246 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8695 (mtt) cc_final: 0.8329 (mtt) REVERT: B 1 MET cc_start: 0.5685 (ttt) cc_final: 0.5331 (ttt) REVERT: C 365 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6852 (mmt90) REVERT: C 409 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7089 (p90) REVERT: F 379 MET cc_start: 0.8436 (tpp) cc_final: 0.8151 (tpp) REVERT: G 31 MET cc_start: 0.8987 (ttp) cc_final: 0.8693 (ttp) REVERT: G 116 MET cc_start: 0.8386 (mpp) cc_final: 0.8154 (mmt) REVERT: H 7 ASP cc_start: 0.6030 (t70) cc_final: 0.5554 (p0) REVERT: H 70 GLU cc_start: 0.4575 (OUTLIER) cc_final: 0.4009 (tp30) REVERT: W 147 MET cc_start: 0.8387 (mmt) cc_final: 0.8036 (mmp) REVERT: I 16 MET cc_start: 0.5175 (ptm) cc_final: 0.4772 (ptm) REVERT: I 17 MET cc_start: 0.4117 (ppp) cc_final: 0.3789 (mtm) REVERT: I 75 MET cc_start: -0.3294 (ttt) cc_final: -0.3717 (ttm) REVERT: J 11 MET cc_start: 0.1070 (mmm) cc_final: 0.0439 (tmm) REVERT: L 17 MET cc_start: 0.0521 (mtm) cc_final: -0.0004 (ttm) REVERT: L 65 MET cc_start: 0.1957 (ptt) cc_final: -0.0245 (tpt) REVERT: M 75 MET cc_start: 0.2248 (tmm) cc_final: 0.1918 (ttt) REVERT: N 6 MET cc_start: -0.0138 (ttp) cc_final: -0.1077 (mpp) REVERT: N 35 PHE cc_start: 0.5781 (t80) cc_final: 0.5473 (t80) REVERT: P 6 MET cc_start: 0.3793 (mmt) cc_final: 0.3342 (ppp) REVERT: P 16 MET cc_start: -0.5188 (ttt) cc_final: -0.5891 (tpt) REVERT: P 65 MET cc_start: -0.2775 (mmt) cc_final: -0.3099 (ptp) REVERT: Q 57 MET cc_start: 0.4386 (tmm) cc_final: 0.3547 (ptm) REVERT: Q 65 MET cc_start: 0.6144 (mtt) cc_final: 0.5321 (tpp) REVERT: R 65 MET cc_start: 0.4042 (mmm) cc_final: 0.3327 (tpt) REVERT: S 35 PHE cc_start: 0.5243 (t80) cc_final: 0.4762 (t80) REVERT: X 73 GLN cc_start: 0.8794 (mp-120) cc_final: 0.8561 (mm-40) REVERT: X 123 GLN cc_start: 0.9013 (mm110) cc_final: 0.8713 (mm-40) REVERT: Y 3 LEU cc_start: -0.2577 (OUTLIER) cc_final: -0.2817 (tp) REVERT: Y 82 ARG cc_start: 0.7227 (mmp80) cc_final: 0.6937 (mmp80) REVERT: Y 98 ARG cc_start: 0.8496 (tpp-160) cc_final: 0.8193 (tpp-160) REVERT: Y 121 ARG cc_start: 0.8782 (tmm-80) cc_final: 0.8527 (tmm-80) outliers start: 48 outliers final: 35 residues processed: 285 average time/residue: 0.5148 time to fit residues: 250.2665 Evaluate side-chains 283 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 244 time to evaluate : 4.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 451 GLU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 78 GLN Chi-restraints excluded: chain Y residue 104 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 5.9990 chunk 449 optimal weight: 0.2980 chunk 274 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 471 optimal weight: 40.0000 chunk 433 optimal weight: 30.0000 chunk 375 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 289 optimal weight: 0.0050 chunk 230 optimal weight: 1.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37493 Z= 0.167 Angle : 0.552 13.083 50750 Z= 0.275 Chirality : 0.040 0.220 5916 Planarity : 0.004 0.045 6545 Dihedral : 6.392 97.086 5366 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.02 % Allowed : 12.86 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.12), residues: 4803 helix: 1.60 (0.11), residues: 2584 sheet: 0.56 (0.22), residues: 531 loop : -0.24 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 513 HIS 0.004 0.001 HIS B 479 PHE 0.018 0.001 PHE S 35 TYR 0.018 0.001 TYR a 263 ARG 0.011 0.000 ARG X 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 246 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8655 (mtp) cc_final: 0.8425 (mtm) REVERT: A 86 MET cc_start: 0.8667 (mtt) cc_final: 0.8231 (mtt) REVERT: B 1 MET cc_start: 0.5819 (ttt) cc_final: 0.5498 (ttt) REVERT: C 365 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6700 (mmt90) REVERT: C 409 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7094 (p90) REVERT: G 31 MET cc_start: 0.8955 (ttp) cc_final: 0.8627 (ttp) REVERT: G 243 MET cc_start: 0.8669 (ttp) cc_final: 0.8317 (ttp) REVERT: H 7 ASP cc_start: 0.6253 (t70) cc_final: 0.5929 (p0) REVERT: H 70 GLU cc_start: 0.4506 (OUTLIER) cc_final: 0.3954 (tp30) REVERT: W 147 MET cc_start: 0.8404 (mmt) cc_final: 0.8031 (mmp) REVERT: I 17 MET cc_start: 0.4261 (ppp) cc_final: 0.3963 (mtm) REVERT: I 75 MET cc_start: -0.3323 (ttt) cc_final: -0.3711 (ttm) REVERT: J 11 MET cc_start: 0.1059 (mmm) cc_final: 0.0407 (tmm) REVERT: L 17 MET cc_start: 0.0317 (mtm) cc_final: -0.0230 (ttm) REVERT: L 65 MET cc_start: 0.1748 (ptt) cc_final: -0.0419 (tpt) REVERT: M 75 MET cc_start: 0.2323 (tmm) cc_final: 0.1963 (ttt) REVERT: N 6 MET cc_start: -0.0439 (ttp) cc_final: -0.1233 (mpp) REVERT: P 6 MET cc_start: 0.3760 (mmt) cc_final: 0.3308 (ppp) REVERT: P 16 MET cc_start: -0.5298 (ttt) cc_final: -0.6006 (tpt) REVERT: P 65 MET cc_start: -0.2893 (mmt) cc_final: -0.3167 (ptp) REVERT: Q 57 MET cc_start: 0.4364 (tmm) cc_final: 0.3560 (ptm) REVERT: Q 65 MET cc_start: 0.6119 (mtt) cc_final: 0.5293 (tpp) REVERT: R 65 MET cc_start: 0.3924 (mmm) cc_final: 0.3253 (tpt) REVERT: S 35 PHE cc_start: 0.5170 (t80) cc_final: 0.4705 (t80) REVERT: X 73 GLN cc_start: 0.8778 (mp-120) cc_final: 0.8526 (mm-40) REVERT: X 115 ARG cc_start: 0.8992 (mtp-110) cc_final: 0.8710 (mtm110) REVERT: X 123 GLN cc_start: 0.8958 (mm110) cc_final: 0.8694 (mm-40) REVERT: Y 3 LEU cc_start: -0.2606 (OUTLIER) cc_final: -0.2841 (tp) REVERT: Y 22 MET cc_start: -0.1735 (tpp) cc_final: -0.2266 (tmm) REVERT: Y 98 ARG cc_start: 0.8508 (tpp-160) cc_final: 0.8210 (tpp-160) REVERT: Y 121 ARG cc_start: 0.8753 (tmm-80) cc_final: 0.8489 (tmm-80) outliers start: 39 outliers final: 23 residues processed: 279 average time/residue: 0.4757 time to fit residues: 222.1705 Evaluate side-chains 268 residues out of total 3836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 241 time to evaluate : 4.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 3.9990 chunk 399 optimal weight: 10.0000 chunk 114 optimal weight: 0.1980 chunk 345 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 104 optimal weight: 0.0570 chunk 375 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 385 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.089432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052084 restraints weight = 144849.649| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.45 r_work: 0.2805 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 37493 Z= 0.138 Angle : 0.539 12.522 50750 Z= 0.268 Chirality : 0.040 0.215 5916 Planarity : 0.004 0.067 6545 Dihedral : 6.039 97.759 5366 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.76 % Allowed : 13.10 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.12), residues: 4803 helix: 1.69 (0.11), residues: 2575 sheet: 0.66 (0.21), residues: 539 loop : -0.20 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 513 HIS 0.003 0.001 HIS B 479 PHE 0.018 0.001 PHE S 35 TYR 0.018 0.001 TYR a 263 ARG 0.017 0.000 ARG J 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7801.38 seconds wall clock time: 140 minutes 58.73 seconds (8458.73 seconds total)