Starting phenix.real_space_refine on Sat Mar 16 01:43:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5t_4418/03_2024/6i5t_4418.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5t_4418/03_2024/6i5t_4418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5t_4418/03_2024/6i5t_4418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5t_4418/03_2024/6i5t_4418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5t_4418/03_2024/6i5t_4418.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i5t_4418/03_2024/6i5t_4418.pdb" } resolution = 3.9 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= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 8550 2.51 5 N 2286 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13356 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "B" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "A" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 510 residue: pdb=" N ARG F 37 " occ=0.97 ... (9 atoms not shown) pdb=" NH2 ARG F 37 " occ=0.93 residue: pdb=" N ALA F 38 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 38 " occ=0.97 residue: pdb=" N VAL F 41 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL F 41 " occ=0.93 residue: pdb=" N GLN F 42 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN F 42 " occ=0.95 residue: pdb=" N ALA F 43 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 43 " occ=0.97 residue: pdb=" N VAL F 46 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL F 46 " occ=0.94 residue: pdb=" N ALA F 52 " occ=0.96 ... (3 atoms not shown) pdb=" CB ALA F 52 " occ=0.93 residue: pdb=" N LYS F 56 " occ=0.97 ... (7 atoms not shown) pdb=" NZ LYS F 56 " occ=0.94 residue: pdb=" N ALA F 57 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 57 " occ=0.97 residue: pdb=" N LEU F 60 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 60 " occ=0.80 residue: pdb=" N GLU F 63 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU F 63 " occ=0.80 residue: pdb=" N ALA F 64 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA F 64 " occ=0.97 ... (remaining 498 not shown) Time building chain proxies: 7.46, per 1000 atoms: 0.56 Number of scatterers: 13356 At special positions: 0 Unit cell: (118.15, 132.6, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2442 8.00 N 2286 7.00 C 8550 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: 4.45 Conformation dependent library (CDL) restraints added in 2.3 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 21 sheets defined 24.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'F' and resid 53 through 66 removed outlier: 3.801A pdb=" N ALA F 57 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG F 120 " --> pdb=" O PRO F 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG F 206 " --> pdb=" O MET F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 226 through 239 removed outlier: 4.432A pdb=" N ALA F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 66 removed outlier: 3.801A pdb=" N ALA E 57 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU E 119 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG E 120 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 173 Processing helix chain 'E' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG E 206 " --> pdb=" O MET E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA E 230 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 66 removed outlier: 3.800A pdb=" N ALA D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP D 102 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG D 120 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG D 206 " --> pdb=" O MET D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.801A pdb=" N ALA C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.800A pdb=" N ALA B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 4.334A pdb=" N ARG B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASP B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.546A pdb=" N GLU B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.801A pdb=" N ALA A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.333A pdb=" N ARG A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASP A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.547A pdb=" N GLU A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 202 through 210 removed outlier: 3.915A pdb=" N ARG A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 226 through 239 removed outlier: 4.433A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 157 through 160 removed outlier: 7.243A pdb=" N PHE F 150 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 72 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU F 71 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'F' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR F 217 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA F 246 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA F 219 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE F 283 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 330 through 334 removed outlier: 3.544A pdb=" N SER E 331 " --> pdb=" O ASN F 333 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER F 331 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N SER D 343 " --> pdb=" O PHE F 330 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU F 332 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LYS D 345 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE F 334 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 157 through 160 removed outlier: 7.242A pdb=" N PHE E 150 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL E 72 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 71 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'E' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR E 217 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA E 246 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA E 219 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE E 283 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 342 through 345 removed outlier: 3.537A pdb=" N SER C 331 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 331 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N SER B 343 " --> pdb=" O PHE D 330 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU D 332 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LYS B 345 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE D 334 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 157 through 160 removed outlier: 7.243A pdb=" N PHE D 150 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 72 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 71 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AB2, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.522A pdb=" N TYR D 217 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA D 246 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA D 219 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE D 283 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 160 removed outlier: 7.243A pdb=" N PHE C 150 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 72 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 71 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AB5, first strand: chain 'C' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR C 217 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA C 246 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA C 219 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE C 283 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 345 removed outlier: 3.557A pdb=" N SER A 331 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 331 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 157 through 160 removed outlier: 7.242A pdb=" N PHE B 150 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 72 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 71 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AB9, first strand: chain 'B' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR B 217 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA B 246 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA B 219 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE B 283 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.243A pdb=" N PHE A 150 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 72 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 71 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AC3, first strand: chain 'A' and resid 186 through 187 removed outlier: 6.523A pdb=" N TYR A 217 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA A 246 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA A 219 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE A 283 " --> pdb=" O LEU A 291 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 936 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: 3.60 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4295 1.34 - 1.46: 2618 1.46 - 1.57: 6629 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 13656 Sorted by residual: bond pdb=" CA HIS E 323 " pdb=" C HIS E 323 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.34e-02 5.57e+03 3.93e+00 bond pdb=" CA HIS B 323 " pdb=" C HIS B 323 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.34e-02 5.57e+03 3.70e+00 bond pdb=" CA HIS C 323 " pdb=" C HIS C 323 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.34e-02 5.57e+03 3.68e+00 bond pdb=" CA HIS A 323 " pdb=" C HIS A 323 " ideal model delta sigma weight residual 1.523 1.549 -0.025 1.34e-02 5.57e+03 3.58e+00 bond pdb=" CA HIS F 323 " pdb=" C HIS F 323 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.34e-02 5.57e+03 3.56e+00 ... (remaining 13651 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.38: 346 105.38 - 112.52: 6699 112.52 - 119.67: 4578 119.67 - 126.82: 6689 126.82 - 133.96: 174 Bond angle restraints: 18486 Sorted by residual: angle pdb=" C VAL E 320 " pdb=" N VAL E 321 " pdb=" CA VAL E 321 " ideal model delta sigma weight residual 121.97 130.89 -8.92 1.80e+00 3.09e-01 2.46e+01 angle pdb=" C VAL C 320 " pdb=" N VAL C 321 " pdb=" CA VAL C 321 " ideal model delta sigma weight residual 121.97 130.86 -8.89 1.80e+00 3.09e-01 2.44e+01 angle pdb=" C VAL A 320 " pdb=" N VAL A 321 " pdb=" CA VAL A 321 " ideal model delta sigma weight residual 121.97 130.86 -8.89 1.80e+00 3.09e-01 2.44e+01 angle pdb=" C VAL D 320 " pdb=" N VAL D 321 " pdb=" CA VAL D 321 " ideal model delta sigma weight residual 121.97 130.84 -8.87 1.80e+00 3.09e-01 2.43e+01 angle pdb=" N VAL D 321 " pdb=" CA VAL D 321 " pdb=" C VAL D 321 " ideal model delta sigma weight residual 109.34 119.58 -10.24 2.08e+00 2.31e-01 2.42e+01 ... (remaining 18481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.53: 7564 14.53 - 29.05: 434 29.05 - 43.58: 96 43.58 - 58.10: 6 58.10 - 72.63: 6 Dihedral angle restraints: 8106 sinusoidal: 3162 harmonic: 4944 Sorted by residual: dihedral pdb=" CA GLY B 322 " pdb=" C GLY B 322 " pdb=" N HIS B 323 " pdb=" CA HIS B 323 " ideal model delta harmonic sigma weight residual -180.00 -107.37 -72.63 0 5.00e+00 4.00e-02 2.11e+02 dihedral pdb=" CA GLY F 322 " pdb=" C GLY F 322 " pdb=" N HIS F 323 " pdb=" CA HIS F 323 " ideal model delta harmonic sigma weight residual -180.00 -107.40 -72.60 0 5.00e+00 4.00e-02 2.11e+02 dihedral pdb=" CA GLY A 322 " pdb=" C GLY A 322 " pdb=" N HIS A 323 " pdb=" CA HIS A 323 " ideal model delta harmonic sigma weight residual -180.00 -107.41 -72.59 0 5.00e+00 4.00e-02 2.11e+02 ... (remaining 8103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1591 0.066 - 0.132: 408 0.132 - 0.198: 29 0.198 - 0.265: 18 0.265 - 0.331: 12 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CB VAL E 320 " pdb=" CA VAL E 320 " pdb=" CG1 VAL E 320 " pdb=" CG2 VAL E 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL A 320 " pdb=" CA VAL A 320 " pdb=" CG1 VAL A 320 " pdb=" CG2 VAL A 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB VAL F 320 " pdb=" CA VAL F 320 " pdb=" CG1 VAL F 320 " pdb=" CG2 VAL F 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2055 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 187 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO F 188 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 188 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 188 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 187 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO A 188 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 187 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO C 188 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " 0.029 5.00e-02 4.00e+02 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4687 2.87 - 3.38: 11187 3.38 - 3.88: 19763 3.88 - 4.39: 22052 4.39 - 4.90: 39536 Nonbonded interactions: 97225 Sorted by model distance: nonbonded pdb=" OE1 GLU A 89 " pdb=" OG1 THR A 96 " model vdw 2.362 2.440 nonbonded pdb=" OE1 GLU E 89 " pdb=" OG1 THR E 96 " model vdw 2.362 2.440 nonbonded pdb=" OE1 GLU F 89 " pdb=" OG1 THR F 96 " model vdw 2.362 2.440 nonbonded pdb=" OE1 GLU D 89 " pdb=" OG1 THR D 96 " model vdw 2.362 2.440 nonbonded pdb=" OE1 GLU C 89 " pdb=" OG1 THR C 96 " model vdw 2.363 2.440 ... (remaining 97220 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.50 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.010 Extract box with map and model: 4.370 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.390 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.006 0.045 13656 Z= 0.402 Angle : 1.110 17.014 18486 Z= 0.584 Chirality : 0.064 0.331 2058 Planarity : 0.008 0.053 2370 Dihedral : 10.098 72.626 4950 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.09 % Favored : 84.21 % Rotamer: Outliers : 0.43 % Allowed : 6.01 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.73 % 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: -5.80 (0.13), residues: 1710 helix: -3.89 (0.13), residues: 438 sheet: -4.21 (0.25), residues: 216 loop : -3.96 (0.13), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 198 HIS 0.007 0.002 HIS F 234 PHE 0.011 0.002 PHE C 316 TYR 0.030 0.003 TYR B 324 ARG 0.005 0.001 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 436 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 138 GLU cc_start: 0.8759 (pt0) cc_final: 0.8275 (pt0) REVERT: F 162 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8348 (mtt180) REVERT: F 221 THR cc_start: 0.9351 (t) cc_final: 0.8951 (m) REVERT: E 134 MET cc_start: 0.7090 (tpp) cc_final: 0.6817 (tpp) REVERT: D 89 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7266 (tt0) REVERT: D 138 GLU cc_start: 0.8764 (pt0) cc_final: 0.8254 (pt0) REVERT: D 221 THR cc_start: 0.9432 (t) cc_final: 0.9027 (m) REVERT: C 285 SER cc_start: 0.8506 (t) cc_final: 0.7628 (p) REVERT: B 138 GLU cc_start: 0.8746 (pt0) cc_final: 0.8078 (pt0) REVERT: B 221 THR cc_start: 0.9407 (t) cc_final: 0.8950 (m) REVERT: B 285 SER cc_start: 0.9045 (t) cc_final: 0.8192 (p) REVERT: B 315 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8183 (tttt) REVERT: A 134 MET cc_start: 0.7057 (tpp) cc_final: 0.6848 (tpp) REVERT: A 167 THR cc_start: 0.8400 (p) cc_final: 0.8195 (m) outliers start: 6 outliers final: 1 residues processed: 436 average time/residue: 0.3048 time to fit residues: 179.5116 Evaluate side-chains 196 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 98 optimal weight: 0.0010 chunk 152 optimal weight: 7.9990 overall best weight: 4.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN F 154 GLN F 200 ASN F 295 ASN E 154 GLN E 200 ASN D 200 ASN D 295 ASN C 200 ASN C 234 HIS B 154 GLN B 200 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13656 Z= 0.299 Angle : 0.764 12.050 18486 Z= 0.386 Chirality : 0.049 0.158 2058 Planarity : 0.006 0.044 2370 Dihedral : 6.510 53.974 1904 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.75 % Favored : 86.20 % Rotamer: Outliers : 5.01 % Allowed : 10.66 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.16), residues: 1710 helix: -2.36 (0.22), residues: 402 sheet: -2.74 (0.27), residues: 300 loop : -3.74 (0.14), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 198 HIS 0.011 0.003 HIS B 323 PHE 0.011 0.002 PHE F 157 TYR 0.019 0.002 TYR D 128 ARG 0.005 0.001 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 205 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 127 LYS cc_start: 0.7730 (pttt) cc_final: 0.6465 (mtpp) REVERT: F 138 GLU cc_start: 0.8832 (pt0) cc_final: 0.8626 (pt0) REVERT: F 169 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8160 (tm) REVERT: F 221 THR cc_start: 0.9293 (t) cc_final: 0.8816 (m) REVERT: F 283 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8975 (mt) REVERT: D 67 ASN cc_start: 0.8320 (p0) cc_final: 0.7802 (t0) REVERT: D 89 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7436 (tt0) REVERT: D 127 LYS cc_start: 0.7695 (pttt) cc_final: 0.6653 (mtpp) REVERT: D 169 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8482 (tm) REVERT: D 221 THR cc_start: 0.9384 (t) cc_final: 0.8977 (m) REVERT: D 227 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8439 (m) REVERT: C 134 MET cc_start: 0.6963 (tpt) cc_final: 0.6710 (tpt) REVERT: C 310 ASP cc_start: 0.7854 (t0) cc_final: 0.7601 (t0) REVERT: B 127 LYS cc_start: 0.7636 (pttt) cc_final: 0.6773 (mtpp) REVERT: B 184 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7597 (p) REVERT: B 221 THR cc_start: 0.9338 (t) cc_final: 0.8928 (m) REVERT: B 227 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8280 (m) REVERT: A 134 MET cc_start: 0.7329 (tpp) cc_final: 0.7092 (tpp) REVERT: A 138 GLU cc_start: 0.8606 (tt0) cc_final: 0.8014 (tt0) outliers start: 70 outliers final: 41 residues processed: 264 average time/residue: 0.2198 time to fit residues: 87.8746 Evaluate side-chains 222 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 175 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 289 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 122 optimal weight: 0.4980 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN F 154 GLN F 295 ASN D 295 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13656 Z= 0.287 Angle : 0.748 12.420 18486 Z= 0.374 Chirality : 0.048 0.175 2058 Planarity : 0.006 0.039 2370 Dihedral : 6.325 47.677 1904 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.92 % Favored : 86.02 % Rotamer: Outliers : 5.72 % Allowed : 11.16 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.17), residues: 1710 helix: -1.84 (0.24), residues: 402 sheet: -2.50 (0.28), residues: 312 loop : -3.53 (0.15), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 198 HIS 0.007 0.002 HIS B 323 PHE 0.010 0.001 PHE F 157 TYR 0.017 0.002 TYR D 128 ARG 0.006 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 192 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: F 127 LYS cc_start: 0.7600 (pttt) cc_final: 0.6673 (mtpp) REVERT: F 138 GLU cc_start: 0.8873 (pt0) cc_final: 0.8651 (pt0) REVERT: F 169 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8267 (tm) REVERT: F 227 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8261 (m) REVERT: D 89 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7538 (tt0) REVERT: D 127 LYS cc_start: 0.7596 (pttt) cc_final: 0.6822 (mtpt) REVERT: D 169 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8526 (tm) REVERT: D 221 THR cc_start: 0.9337 (t) cc_final: 0.8944 (m) REVERT: D 227 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8489 (m) REVERT: C 138 GLU cc_start: 0.8469 (tt0) cc_final: 0.8157 (tt0) REVERT: B 127 LYS cc_start: 0.7749 (pttt) cc_final: 0.6949 (mtpp) REVERT: B 221 THR cc_start: 0.9326 (t) cc_final: 0.8905 (m) REVERT: B 227 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8213 (m) outliers start: 80 outliers final: 49 residues processed: 259 average time/residue: 0.2215 time to fit residues: 89.1636 Evaluate side-chains 212 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 158 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 153 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 30.0000 overall best weight: 2.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 154 GLN F 295 ASN E 234 HIS D 295 ASN C 295 ASN B 295 ASN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13656 Z= 0.214 Angle : 0.700 12.238 18486 Z= 0.348 Chirality : 0.047 0.177 2058 Planarity : 0.005 0.036 2370 Dihedral : 5.982 47.913 1904 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.16 % Favored : 86.78 % Rotamer: Outliers : 5.72 % Allowed : 13.23 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.18), residues: 1710 helix: -1.49 (0.25), residues: 402 sheet: -2.10 (0.29), residues: 342 loop : -3.45 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 198 HIS 0.008 0.002 HIS A 323 PHE 0.008 0.001 PHE A 103 TYR 0.015 0.001 TYR D 128 ARG 0.004 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 197 time to evaluate : 1.484 Fit side-chains REVERT: F 127 LYS cc_start: 0.7634 (pttt) cc_final: 0.6906 (mtpp) REVERT: F 129 LYS cc_start: 0.7704 (mmtt) cc_final: 0.7308 (mmtm) REVERT: F 138 GLU cc_start: 0.8879 (pt0) cc_final: 0.8628 (pt0) REVERT: F 169 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8194 (tm) REVERT: F 227 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8075 (m) REVERT: E 138 GLU cc_start: 0.8504 (tt0) cc_final: 0.7898 (tt0) REVERT: E 232 MET cc_start: 0.8939 (mmm) cc_final: 0.7608 (mmm) REVERT: D 89 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7526 (tt0) REVERT: D 127 LYS cc_start: 0.7590 (pttt) cc_final: 0.6755 (mtpp) REVERT: D 134 MET cc_start: 0.7778 (mmm) cc_final: 0.7546 (tpt) REVERT: D 169 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8362 (tm) REVERT: D 227 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8175 (m) REVERT: D 287 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8753 (mt) REVERT: C 138 GLU cc_start: 0.8445 (tt0) cc_final: 0.8117 (tt0) REVERT: B 127 LYS cc_start: 0.7726 (pttt) cc_final: 0.6956 (mtpp) REVERT: B 227 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.7968 (m) REVERT: B 324 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7594 (t80) REVERT: A 138 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8316 (tt0) outliers start: 80 outliers final: 51 residues processed: 264 average time/residue: 0.2111 time to fit residues: 85.1214 Evaluate side-chains 226 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 167 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 7.9990 chunk 92 optimal weight: 0.0020 chunk 2 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 overall best weight: 3.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN E 295 ASN D 67 ASN D 295 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13656 Z= 0.245 Angle : 0.721 12.336 18486 Z= 0.356 Chirality : 0.048 0.192 2058 Planarity : 0.005 0.033 2370 Dihedral : 5.978 50.164 1904 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 1.05 % Allowed : 13.04 % Favored : 85.91 % Rotamer: Outliers : 6.15 % Allowed : 14.81 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.18), residues: 1710 helix: -1.32 (0.25), residues: 402 sheet: -1.93 (0.29), residues: 342 loop : -3.36 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 198 HIS 0.006 0.001 HIS F 323 PHE 0.009 0.001 PHE A 103 TYR 0.021 0.001 TYR C 296 ARG 0.003 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 185 time to evaluate : 1.584 Fit side-chains REVERT: F 127 LYS cc_start: 0.7860 (pttt) cc_final: 0.7033 (mtpp) REVERT: F 169 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8245 (tm) REVERT: F 227 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8152 (m) REVERT: F 324 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7815 (t80) REVERT: E 138 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: E 144 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9011 (mt) REVERT: E 232 MET cc_start: 0.8974 (mmm) cc_final: 0.7663 (mmm) REVERT: E 324 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6789 (t80) REVERT: D 89 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7571 (tt0) REVERT: D 127 LYS cc_start: 0.7494 (pttt) cc_final: 0.6843 (mtpt) REVERT: D 134 MET cc_start: 0.7798 (mmm) cc_final: 0.7597 (tpt) REVERT: D 169 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8502 (tm) REVERT: D 227 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8184 (m) REVERT: D 324 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7524 (t80) REVERT: C 134 MET cc_start: 0.7451 (mmm) cc_final: 0.6922 (tpt) REVERT: C 138 GLU cc_start: 0.8397 (tt0) cc_final: 0.8102 (tt0) REVERT: C 140 GLU cc_start: 0.7608 (tt0) cc_final: 0.7399 (tt0) REVERT: B 127 LYS cc_start: 0.7561 (pttt) cc_final: 0.6909 (mtpp) REVERT: B 227 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8030 (m) REVERT: B 324 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7704 (t80) REVERT: A 138 GLU cc_start: 0.8704 (tt0) cc_final: 0.8110 (tt0) outliers start: 86 outliers final: 60 residues processed: 256 average time/residue: 0.2163 time to fit residues: 84.9746 Evaluate side-chains 239 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 168 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN F 337 HIS D 67 ASN D 295 ASN B 295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13656 Z= 0.372 Angle : 0.792 12.287 18486 Z= 0.398 Chirality : 0.050 0.200 2058 Planarity : 0.005 0.035 2370 Dihedral : 6.338 51.199 1904 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 1.05 % Allowed : 14.50 % Favored : 84.44 % Rotamer: Outliers : 6.44 % Allowed : 15.59 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.18), residues: 1710 helix: -1.71 (0.24), residues: 432 sheet: -1.77 (0.29), residues: 330 loop : -3.46 (0.16), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 198 HIS 0.005 0.002 HIS F 323 PHE 0.013 0.002 PHE C 330 TYR 0.017 0.002 TYR C 296 ARG 0.003 0.000 ARG D 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 167 time to evaluate : 1.591 Fit side-chains REVERT: F 61 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8874 (tt) REVERT: F 127 LYS cc_start: 0.7785 (pttt) cc_final: 0.7216 (mtpp) REVERT: F 227 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8272 (m) REVERT: F 324 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7866 (t80) REVERT: E 144 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9080 (mt) REVERT: E 310 ASP cc_start: 0.8015 (t0) cc_final: 0.7781 (t0) REVERT: E 324 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.6722 (t80) REVERT: D 89 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7593 (tt0) REVERT: D 127 LYS cc_start: 0.7611 (pttt) cc_final: 0.6972 (mtpt) REVERT: D 134 MET cc_start: 0.7839 (mmm) cc_final: 0.7589 (tpt) REVERT: D 169 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8621 (tm) REVERT: D 232 MET cc_start: 0.8839 (mmm) cc_final: 0.7804 (mmm) REVERT: D 324 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7533 (t80) REVERT: C 134 MET cc_start: 0.7356 (mmm) cc_final: 0.6927 (tpt) REVERT: C 138 GLU cc_start: 0.8431 (tt0) cc_final: 0.8077 (tt0) REVERT: C 310 ASP cc_start: 0.7948 (t0) cc_final: 0.7746 (t0) REVERT: B 127 LYS cc_start: 0.7775 (pttt) cc_final: 0.7377 (mtpp) REVERT: B 129 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7244 (mmtp) REVERT: B 227 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8242 (m) REVERT: B 324 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7868 (t80) REVERT: A 134 MET cc_start: 0.6822 (tpp) cc_final: 0.6587 (tpt) REVERT: A 138 GLU cc_start: 0.8720 (tt0) cc_final: 0.8319 (tt0) REVERT: A 324 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6764 (t80) outliers start: 90 outliers final: 65 residues processed: 240 average time/residue: 0.2094 time to fit residues: 77.1266 Evaluate side-chains 230 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 155 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN D 295 ASN B 295 ASN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13656 Z= 0.238 Angle : 0.715 12.673 18486 Z= 0.354 Chirality : 0.047 0.165 2058 Planarity : 0.005 0.034 2370 Dihedral : 5.970 51.363 1904 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.11 % Favored : 86.84 % Rotamer: Outliers : 6.15 % Allowed : 16.60 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.19), residues: 1710 helix: -1.20 (0.26), residues: 402 sheet: -1.77 (0.29), residues: 342 loop : -3.30 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 198 HIS 0.007 0.001 HIS F 323 PHE 0.013 0.001 PHE C 330 TYR 0.015 0.001 TYR C 296 ARG 0.003 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 181 time to evaluate : 1.428 Fit side-chains REVERT: F 61 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8803 (tt) REVERT: F 127 LYS cc_start: 0.8014 (pttt) cc_final: 0.7321 (mtpp) REVERT: F 169 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8264 (tm) REVERT: F 227 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8073 (m) REVERT: F 324 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7905 (t80) REVERT: E 134 MET cc_start: 0.6989 (tpp) cc_final: 0.6780 (tpp) REVERT: E 138 GLU cc_start: 0.8583 (tt0) cc_final: 0.8072 (tt0) REVERT: E 310 ASP cc_start: 0.8044 (t0) cc_final: 0.7801 (t0) REVERT: E 324 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.6731 (t80) REVERT: D 89 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7614 (tt0) REVERT: D 127 LYS cc_start: 0.7687 (pttt) cc_final: 0.7183 (mtpp) REVERT: D 134 MET cc_start: 0.7827 (mmm) cc_final: 0.7554 (tpt) REVERT: D 169 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8479 (tm) REVERT: D 232 MET cc_start: 0.8854 (mmm) cc_final: 0.7782 (mmm) REVERT: D 324 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7721 (t80) REVERT: C 134 MET cc_start: 0.7337 (mmm) cc_final: 0.6989 (tpt) REVERT: C 138 GLU cc_start: 0.8426 (tt0) cc_final: 0.8200 (tt0) REVERT: B 127 LYS cc_start: 0.7852 (pttt) cc_final: 0.7393 (mtpp) REVERT: B 129 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7249 (mmtp) REVERT: B 227 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8088 (m) REVERT: B 324 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7823 (t80) REVERT: A 138 GLU cc_start: 0.8675 (tt0) cc_final: 0.8316 (tt0) REVERT: A 324 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.6799 (t80) outliers start: 86 outliers final: 66 residues processed: 249 average time/residue: 0.2038 time to fit residues: 78.1414 Evaluate side-chains 246 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 170 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 295 ASN D 295 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 HIS B 295 ASN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13656 Z= 0.362 Angle : 0.792 12.523 18486 Z= 0.396 Chirality : 0.050 0.208 2058 Planarity : 0.005 0.036 2370 Dihedral : 6.324 52.417 1904 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 1.05 % Allowed : 14.91 % Favored : 84.04 % Rotamer: Outliers : 6.22 % Allowed : 16.52 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.18), residues: 1710 helix: -1.59 (0.24), residues: 432 sheet: -1.67 (0.30), residues: 330 loop : -3.41 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 198 HIS 0.005 0.002 HIS D 323 PHE 0.012 0.002 PHE F 318 TYR 0.016 0.002 TYR C 296 ARG 0.004 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 165 time to evaluate : 1.568 Fit side-chains REVERT: F 61 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8856 (tt) REVERT: F 127 LYS cc_start: 0.8127 (pttt) cc_final: 0.7230 (mtpp) REVERT: F 227 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8290 (m) REVERT: F 324 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7920 (t80) REVERT: E 232 MET cc_start: 0.9022 (mmm) cc_final: 0.7776 (mmm) REVERT: E 310 ASP cc_start: 0.8159 (t0) cc_final: 0.7943 (t0) REVERT: E 324 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.6783 (t80) REVERT: D 89 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7587 (tt0) REVERT: D 127 LYS cc_start: 0.7681 (pttt) cc_final: 0.7173 (mtpp) REVERT: D 134 MET cc_start: 0.7843 (mmm) cc_final: 0.7587 (tpt) REVERT: D 169 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8606 (tm) REVERT: D 232 MET cc_start: 0.8883 (mmm) cc_final: 0.7822 (mmm) REVERT: D 324 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7612 (t80) REVERT: C 134 MET cc_start: 0.7311 (mmm) cc_final: 0.6981 (tpt) REVERT: C 138 GLU cc_start: 0.8425 (tt0) cc_final: 0.8058 (tt0) REVERT: B 127 LYS cc_start: 0.7910 (pttt) cc_final: 0.7483 (mtpp) REVERT: B 227 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8269 (m) REVERT: B 324 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7967 (t80) REVERT: A 138 GLU cc_start: 0.8716 (tt0) cc_final: 0.8327 (tt0) REVERT: A 324 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6829 (t80) outliers start: 87 outliers final: 68 residues processed: 236 average time/residue: 0.2094 time to fit residues: 75.2092 Evaluate side-chains 232 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 155 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 150 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 chunk 136 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 295 ASN B 67 ASN B 295 ASN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13656 Z= 0.201 Angle : 0.706 12.502 18486 Z= 0.350 Chirality : 0.047 0.174 2058 Planarity : 0.004 0.033 2370 Dihedral : 5.796 51.189 1904 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.29 % Favored : 87.66 % Rotamer: Outliers : 5.29 % Allowed : 17.81 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.19), residues: 1710 helix: -1.04 (0.26), residues: 402 sheet: -1.55 (0.30), residues: 342 loop : -3.24 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.008 0.001 HIS D 323 PHE 0.012 0.001 PHE C 330 TYR 0.014 0.001 TYR C 296 ARG 0.003 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 188 time to evaluate : 1.516 Fit side-chains REVERT: F 61 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8783 (tt) REVERT: F 127 LYS cc_start: 0.7905 (pttt) cc_final: 0.7473 (mtpp) REVERT: F 129 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7357 (mmtp) REVERT: F 169 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8168 (tm) REVERT: F 324 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7893 (t80) REVERT: E 324 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.6756 (t80) REVERT: D 89 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7594 (tt0) REVERT: D 127 LYS cc_start: 0.7663 (pttt) cc_final: 0.7174 (mtpp) REVERT: D 134 MET cc_start: 0.7825 (mmm) cc_final: 0.7596 (tpt) REVERT: D 169 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8461 (tm) REVERT: D 232 MET cc_start: 0.8851 (mmm) cc_final: 0.7786 (mmm) REVERT: D 324 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.7627 (t80) REVERT: C 134 MET cc_start: 0.7393 (mmm) cc_final: 0.7103 (tpt) REVERT: C 138 GLU cc_start: 0.8406 (tt0) cc_final: 0.8178 (tt0) REVERT: B 127 LYS cc_start: 0.7876 (pttt) cc_final: 0.7485 (mtpp) REVERT: B 129 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7329 (mmtp) REVERT: B 227 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8077 (m) REVERT: B 324 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7740 (t80) REVERT: A 138 GLU cc_start: 0.8649 (tt0) cc_final: 0.8333 (tt0) REVERT: A 324 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.6858 (t80) outliers start: 74 outliers final: 57 residues processed: 247 average time/residue: 0.2110 time to fit residues: 80.0172 Evaluate side-chains 238 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 172 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 324 TYR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN B 295 ASN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13656 Z= 0.182 Angle : 0.691 12.807 18486 Z= 0.340 Chirality : 0.046 0.172 2058 Planarity : 0.004 0.033 2370 Dihedral : 5.543 50.310 1904 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.58 % Favored : 87.37 % Rotamer: Outliers : 4.65 % Allowed : 18.60 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.19), residues: 1710 helix: -0.97 (0.26), residues: 408 sheet: -1.13 (0.29), residues: 378 loop : -3.27 (0.17), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 198 HIS 0.007 0.001 HIS D 323 PHE 0.011 0.001 PHE A 185 TYR 0.016 0.001 TYR C 296 ARG 0.003 0.000 ARG F 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 190 time to evaluate : 1.483 Fit side-chains REVERT: F 61 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8697 (tt) REVERT: F 127 LYS cc_start: 0.8171 (pttt) cc_final: 0.7543 (mtpp) REVERT: F 129 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7335 (mmtp) REVERT: F 169 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8016 (tm) REVERT: E 134 MET cc_start: 0.6873 (tpp) cc_final: 0.6624 (mmm) REVERT: E 138 GLU cc_start: 0.8553 (tt0) cc_final: 0.8116 (tt0) REVERT: E 310 ASP cc_start: 0.8120 (t0) cc_final: 0.7766 (t0) REVERT: E 324 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.6898 (t80) REVERT: D 89 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7596 (tt0) REVERT: D 127 LYS cc_start: 0.7645 (pttt) cc_final: 0.7171 (mtpt) REVERT: D 134 MET cc_start: 0.7789 (mmm) cc_final: 0.7546 (tpt) REVERT: D 169 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8327 (tm) REVERT: D 232 MET cc_start: 0.8838 (mmm) cc_final: 0.7732 (mmm) REVERT: D 324 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7696 (t80) REVERT: C 134 MET cc_start: 0.7365 (mmm) cc_final: 0.6943 (tpt) REVERT: C 138 GLU cc_start: 0.8376 (tt0) cc_final: 0.8132 (tt0) REVERT: B 129 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7382 (mmtp) REVERT: B 324 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7599 (t80) REVERT: A 138 GLU cc_start: 0.8587 (tt0) cc_final: 0.8121 (tt0) REVERT: A 324 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6848 (t80) outliers start: 65 outliers final: 48 residues processed: 241 average time/residue: 0.2064 time to fit residues: 77.0274 Evaluate side-chains 235 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 180 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 324 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 324 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN B 295 ASN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.120166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.102292 restraints weight = 21525.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.103968 restraints weight = 16162.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.105102 restraints weight = 13241.260| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 40 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13656 Z= 0.279 Angle : 0.756 12.765 18486 Z= 0.372 Chirality : 0.048 0.210 2058 Planarity : 0.005 0.032 2370 Dihedral : 5.864 51.012 1904 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 1.05 % Allowed : 13.51 % Favored : 85.44 % Rotamer: Outliers : 4.86 % Allowed : 18.81 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.19), residues: 1710 helix: -0.91 (0.26), residues: 402 sheet: -1.57 (0.30), residues: 336 loop : -3.24 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 198 HIS 0.006 0.001 HIS F 323 PHE 0.010 0.002 PHE A 103 TYR 0.018 0.001 TYR E 106 ARG 0.006 0.000 ARG B 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2634.97 seconds wall clock time: 48 minutes 20.58 seconds (2900.58 seconds total)