Starting phenix.real_space_refine on Mon May 26 02:35:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgn_44518/05_2025/9bgn_44518.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgn_44518/05_2025/9bgn_44518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgn_44518/05_2025/9bgn_44518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgn_44518/05_2025/9bgn_44518.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgn_44518/05_2025/9bgn_44518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgn_44518/05_2025/9bgn_44518.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 171 5.16 5 C 17595 2.51 5 N 4824 2.21 5 O 5265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 256 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27855 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "D" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "E" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "F" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "H" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "I" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "A" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "B" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "G" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3095 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Time building chain proxies: 16.64, per 1000 atoms: 0.60 Number of scatterers: 27855 At special positions: 0 Unit cell: (249.76, 294.56, 173.6, 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 171 16.00 O 5265 8.00 N 4824 7.00 C 17595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 3.4 seconds 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6498 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 48 sheets defined 20.8% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'C' and resid 57 through 61 removed outlier: 4.018A pdb=" N TYR C 60 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY C 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 61' Processing helix chain 'C' and resid 101 through 108 Processing helix chain 'C' and resid 144 through 150 Processing helix chain 'C' and resid 154 through 182 removed outlier: 3.795A pdb=" N HIS C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.583A pdb=" N VAL C 198 " --> pdb=" O ASP C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 219 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.777A pdb=" N ILE C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 108 removed outlier: 3.578A pdb=" N LYS D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 154 through 182 removed outlier: 3.546A pdb=" N HIS D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 271 through 277 removed outlier: 4.155A pdb=" N ALA D 274 " --> pdb=" O GLU D 271 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA D 275 " --> pdb=" O LYS D 272 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 276 " --> pdb=" O TYR D 273 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY D 277 " --> pdb=" O ALA D 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 277' Processing helix chain 'D' and resid 358 through 362 removed outlier: 3.627A pdb=" N THR D 361 " --> pdb=" O GLY D 358 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 362 " --> pdb=" O GLU D 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 358 through 362' Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'E' and resid 57 through 61 removed outlier: 4.001A pdb=" N TYR E 60 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY E 61 " --> pdb=" O LYS E 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 57 through 61' Processing helix chain 'E' and resid 101 through 108 Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 154 through 182 removed outlier: 3.691A pdb=" N HIS E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU E 169 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 170 " --> pdb=" O GLY E 166 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 251 through 257 removed outlier: 3.542A pdb=" N ALA E 257 " --> pdb=" O PRO E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 358 through 362 removed outlier: 3.634A pdb=" N THR E 361 " --> pdb=" O GLY E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'F' and resid 46 through 51 removed outlier: 3.692A pdb=" N GLN F 49 " --> pdb=" O TYR F 46 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 144 through 149 Processing helix chain 'F' and resid 154 through 182 removed outlier: 3.578A pdb=" N HIS F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU F 169 " --> pdb=" O LYS F 165 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE F 170 " --> pdb=" O GLY F 166 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 198 removed outlier: 3.648A pdb=" N GLU F 197 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL F 198 " --> pdb=" O ASP F 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 194 through 198' Processing helix chain 'F' and resid 205 through 219 removed outlier: 3.518A pdb=" N ALA F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 358 through 362 removed outlier: 3.798A pdb=" N THR F 361 " --> pdb=" O GLY F 358 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA F 362 " --> pdb=" O GLU F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 362' Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'H' and resid 46 through 51 removed outlier: 3.863A pdb=" N GLN H 49 " --> pdb=" O TYR H 46 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA H 51 " --> pdb=" O GLY H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 108 Processing helix chain 'H' and resid 144 through 149 removed outlier: 3.617A pdb=" N ASP H 148 " --> pdb=" O GLN H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 182 removed outlier: 3.552A pdb=" N HIS H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 169 " --> pdb=" O LYS H 165 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE H 170 " --> pdb=" O GLY H 166 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR H 171 " --> pdb=" O ALA H 167 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU H 172 " --> pdb=" O ASN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 219 Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 271 through 273 No H-bonds generated for 'chain 'H' and resid 271 through 273' Processing helix chain 'H' and resid 358 through 362 removed outlier: 3.538A pdb=" N THR H 361 " --> pdb=" O GLY H 358 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA H 362 " --> pdb=" O GLU H 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 358 through 362' Processing helix chain 'H' and resid 386 through 390 removed outlier: 3.891A pdb=" N ILE H 390 " --> pdb=" O PRO H 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 51 removed outlier: 3.593A pdb=" N LEU I 50 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA I 51 " --> pdb=" O GLY I 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 47 through 51' Processing helix chain 'I' and resid 101 through 106 Processing helix chain 'I' and resid 144 through 149 Processing helix chain 'I' and resid 154 through 182 removed outlier: 3.738A pdb=" N HIS I 158 " --> pdb=" O ALA I 154 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU I 169 " --> pdb=" O LYS I 165 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE I 170 " --> pdb=" O GLY I 166 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR I 171 " --> pdb=" O ALA I 167 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 198 removed outlier: 3.717A pdb=" N GLU I 197 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL I 198 " --> pdb=" O ASP I 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 194 through 198' Processing helix chain 'I' and resid 205 through 219 Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 271 through 273 No H-bonds generated for 'chain 'I' and resid 271 through 273' Processing helix chain 'I' and resid 358 through 362 removed outlier: 3.604A pdb=" N ALA I 362 " --> pdb=" O GLU I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 388 No H-bonds generated for 'chain 'I' and resid 386 through 388' Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.621A pdb=" N GLN A 49 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 51 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 154 through 180 removed outlier: 3.588A pdb=" N HIS A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.834A pdb=" N ALA A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.568A pdb=" N ALA A 274 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA A 275 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 277 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.539A pdb=" N ALA A 362 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.737A pdb=" N LEU B 50 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 154 through 182 removed outlier: 3.712A pdb=" N HIS B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.525A pdb=" N ALA B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.555A pdb=" N LEU G 50 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA G 51 " --> pdb=" O GLY G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 47 through 51' Processing helix chain 'G' and resid 144 through 149 removed outlier: 3.627A pdb=" N ASP G 148 " --> pdb=" O GLN G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 181 removed outlier: 4.153A pdb=" N HIS G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU G 169 " --> pdb=" O LYS G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 219 Processing helix chain 'G' and resid 248 through 250 No H-bonds generated for 'chain 'G' and resid 248 through 250' Processing helix chain 'G' and resid 251 through 256 removed outlier: 3.580A pdb=" N ILE G 255 " --> pdb=" O LEU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 273 No H-bonds generated for 'chain 'G' and resid 271 through 273' Processing helix chain 'G' and resid 358 through 362 removed outlier: 3.542A pdb=" N THR G 361 " --> pdb=" O GLY G 358 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 362 " --> pdb=" O GLU G 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 358 through 362' Processing helix chain 'G' and resid 386 through 389 Processing sheet with id=AA1, first strand: chain 'C' and resid 32 through 33 removed outlier: 6.550A pdb=" N TYR C 32 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU B 67 " --> pdb=" O TYR C 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 32 through 33 removed outlier: 6.550A pdb=" N TYR C 32 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU B 67 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS B 125 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.858A pdb=" N VAL C 65 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ARG D 36 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU C 67 " --> pdb=" O ARG D 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.878A pdb=" N ALA C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 134 through 143 Processing sheet with id=AA7, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA8, first strand: chain 'C' and resid 243 through 247 removed outlier: 4.106A pdb=" N GLY C 285 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 294 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU C 283 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 55 removed outlier: 4.672A pdb=" N VAL D 384 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LYS D 130 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS D 125 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 187 removed outlier: 3.503A pdb=" N LYS D 394 " --> pdb=" O ARG D 187 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY D 248 " --> pdb=" O PRO D 327 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL D 331 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA D 244 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE D 290 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN D 286 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL D 292 " --> pdb=" O VAL D 284 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 318 through 319 Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 39 removed outlier: 4.667A pdb=" N LEU F 67 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG E 36 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N TYR F 69 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU E 38 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 55 removed outlier: 6.383A pdb=" N PHE E 54 " --> pdb=" O GLY E 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 53 through 55 removed outlier: 6.383A pdb=" N PHE E 54 " --> pdb=" O GLY E 340 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 65 through 70 removed outlier: 4.585A pdb=" N LYS E 125 " --> pdb=" O ILE E 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 82 through 83 removed outlier: 3.698A pdb=" N GLY E 82 " --> pdb=" O ILE E 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.979A pdb=" N VAL E 331 " --> pdb=" O ALA E 244 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA E 244 " --> pdb=" O VAL E 331 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN E 286 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL E 292 " --> pdb=" O VAL E 284 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 318 through 319 Processing sheet with id=AC3, first strand: chain 'F' and resid 32 through 38 removed outlier: 4.716A pdb=" N LEU G 67 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG F 36 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N TYR G 69 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU F 38 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 64 " --> pdb=" O GLY G 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 32 through 38 removed outlier: 4.716A pdb=" N LEU G 67 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG F 36 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N TYR G 69 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU F 38 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 64 " --> pdb=" O GLY G 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'F' and resid 186 through 187 removed outlier: 6.709A pdb=" N ARG F 187 " --> pdb=" O LYS F 394 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR F 323 " --> pdb=" O GLY F 303 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 268 through 269 removed outlier: 6.403A pdb=" N GLU F 283 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL F 294 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY F 285 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA F 244 " --> pdb=" O VAL F 331 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL F 331 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY F 248 " --> pdb=" O PRO F 327 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 53 through 55 Processing sheet with id=AD1, first strand: chain 'H' and resid 53 through 55 removed outlier: 6.466A pdb=" N GLU H 63 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N TYR I 34 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL H 65 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ARG I 36 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU H 67 " --> pdb=" O ARG I 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 186 through 187 removed outlier: 6.689A pdb=" N PHE H 290 " --> pdb=" O GLN H 286 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLN H 286 " --> pdb=" O PHE H 290 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL H 292 " --> pdb=" O VAL H 284 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 318 through 319 Processing sheet with id=AD4, first strand: chain 'I' and resid 53 through 55 removed outlier: 4.915A pdb=" N VAL I 384 " --> pdb=" O LYS I 130 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS I 130 " --> pdb=" O VAL I 384 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD6, first strand: chain 'I' and resid 186 through 187 removed outlier: 6.742A pdb=" N ARG I 187 " --> pdb=" O LYS I 394 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TYR I 323 " --> pdb=" O GLY I 303 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 268 through 269 removed outlier: 6.934A pdb=" N VAL I 292 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN I 286 " --> pdb=" O PHE I 290 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE I 290 " --> pdb=" O GLN I 286 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA I 244 " --> pdb=" O VAL I 331 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL I 331 " --> pdb=" O ALA I 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.198A pdb=" N PHE A 54 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N PHE A 341 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR A 379 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.198A pdb=" N PHE A 54 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N PHE A 341 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR A 379 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 65 through 68 Processing sheet with id=AE2, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.504A pdb=" N GLY A 82 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP A 84 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 186 through 187 removed outlier: 4.625A pdb=" N VAL A 331 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA A 244 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 285 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 294 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU A 283 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AE5, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.962A pdb=" N PHE B 54 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N PHE B 341 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR B 379 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.962A pdb=" N PHE B 54 " --> pdb=" O GLY B 340 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N PHE B 341 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR B 379 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AE8, first strand: chain 'B' and resid 186 through 187 removed outlier: 6.731A pdb=" N ARG B 187 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL B 331 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 244 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG B 243 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE B 293 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU B 245 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLN B 286 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 292 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AF1, first strand: chain 'G' and resid 185 through 187 removed outlier: 6.384A pdb=" N THR G 185 " --> pdb=" O LEU G 392 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LYS G 394 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG G 187 " --> pdb=" O LYS G 394 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 243 through 247 removed outlier: 6.425A pdb=" N PHE G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN G 286 " --> pdb=" O PHE G 290 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL G 292 " --> pdb=" O VAL G 284 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 318 through 319 845 hydrogen bonds defined for protein. 2313 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: 9.97 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9268 1.35 - 1.46: 6300 1.46 - 1.58: 12557 1.58 - 1.70: 0 1.70 - 1.82: 333 Bond restraints: 28458 Sorted by residual: bond pdb=" CG PRO A 315 " pdb=" CD PRO A 315 " ideal model delta sigma weight residual 1.503 1.321 0.182 3.40e-02 8.65e+02 2.87e+01 bond pdb=" N ARG G 398 " pdb=" CA ARG G 398 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.41e-02 5.03e+03 6.14e+00 bond pdb=" N ARG F 398 " pdb=" CA ARG F 398 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.45e-02 4.76e+03 5.66e+00 bond pdb=" N ARG A 398 " pdb=" CA ARG A 398 " ideal model delta sigma weight residual 1.462 1.492 -0.031 1.31e-02 5.83e+03 5.47e+00 bond pdb=" N ARG E 398 " pdb=" CA ARG E 398 " ideal model delta sigma weight residual 1.462 1.489 -0.028 1.31e-02 5.83e+03 4.46e+00 ... (remaining 28453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 38274 2.77 - 5.54: 214 5.54 - 8.31: 7 8.31 - 11.09: 6 11.09 - 13.86: 1 Bond angle restraints: 38502 Sorted by residual: angle pdb=" N PRO A 315 " pdb=" CD PRO A 315 " pdb=" CG PRO A 315 " ideal model delta sigma weight residual 103.20 89.34 13.86 1.50e+00 4.44e-01 8.54e+01 angle pdb=" CA PRO A 315 " pdb=" N PRO A 315 " pdb=" CD PRO A 315 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.77e+01 angle pdb=" CA PRO A 315 " pdb=" CB PRO A 315 " pdb=" CG PRO A 315 " ideal model delta sigma weight residual 104.50 95.56 8.94 1.90e+00 2.77e-01 2.21e+01 angle pdb=" N VAL H 284 " pdb=" CA VAL H 284 " pdb=" C VAL H 284 " ideal model delta sigma weight residual 113.71 109.50 4.21 9.50e-01 1.11e+00 1.96e+01 angle pdb=" N ASP C 6 " pdb=" CA ASP C 6 " pdb=" C ASP C 6 " ideal model delta sigma weight residual 107.73 113.40 -5.67 1.34e+00 5.57e-01 1.79e+01 ... (remaining 38497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14820 17.99 - 35.99: 1743 35.99 - 53.98: 418 53.98 - 71.98: 66 71.98 - 89.97: 26 Dihedral angle restraints: 17073 sinusoidal: 6840 harmonic: 10233 Sorted by residual: dihedral pdb=" CA THR D 279 " pdb=" C THR D 279 " pdb=" N MET D 280 " pdb=" CA MET D 280 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA THR B 279 " pdb=" C THR B 279 " pdb=" N MET B 280 " pdb=" CA MET B 280 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ALA H 397 " pdb=" C ALA H 397 " pdb=" N ARG H 398 " pdb=" CA ARG H 398 " ideal model delta harmonic sigma weight residual 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 17070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2574 0.031 - 0.063: 1016 0.063 - 0.094: 342 0.094 - 0.125: 216 0.125 - 0.157: 28 Chirality restraints: 4176 Sorted by residual: chirality pdb=" CA VAL I 127 " pdb=" N VAL I 127 " pdb=" C VAL I 127 " pdb=" CB VAL I 127 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA VAL F 127 " pdb=" N VAL F 127 " pdb=" C VAL F 127 " pdb=" CB VAL F 127 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA MET E 328 " pdb=" N MET E 328 " pdb=" C MET E 328 " pdb=" CB MET E 328 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 4173 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 397 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ALA H 397 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA H 397 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG H 398 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 397 " 0.019 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ALA I 397 " -0.064 2.00e-02 2.50e+03 pdb=" O ALA I 397 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG I 398 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 397 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ALA E 397 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA E 397 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG E 398 " 0.021 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1102 2.72 - 3.26: 25602 3.26 - 3.81: 39668 3.81 - 4.35: 48928 4.35 - 4.90: 86490 Nonbonded interactions: 201790 Sorted by model distance: nonbonded pdb=" O ALA B 192 " pdb=" OG1 THR B 193 " model vdw 2.170 3.040 nonbonded pdb=" OG SER G 22 " pdb=" O GLY G 25 " model vdw 2.180 3.040 nonbonded pdb=" N GLN E 313 " pdb=" OE1 GLN E 313 " model vdw 2.237 3.120 nonbonded pdb=" O ILE A 225 " pdb=" OG1 THR A 238 " model vdw 2.249 3.040 nonbonded pdb=" O ASP F 52 " pdb=" OG1 THR F 338 " model vdw 2.275 3.040 ... (remaining 201785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 58.670 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.002 0.182 28458 Z= 0.120 Angle : 0.540 13.858 38502 Z= 0.302 Chirality : 0.043 0.157 4176 Planarity : 0.004 0.070 5040 Dihedral : 16.235 89.969 10575 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.42 % Favored : 91.49 % Rotamer: Outliers : 0.14 % Allowed : 21.78 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3573 helix: 1.97 (0.24), residues: 589 sheet: -0.37 (0.20), residues: 619 loop : -2.46 (0.11), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 378 HIS 0.009 0.001 HIS A 317 PHE 0.010 0.001 PHE C 373 TYR 0.016 0.001 TYR E 96 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.15899 ( 789) hydrogen bonds : angle 6.07670 ( 2313) covalent geometry : bond 0.00238 (28458) covalent geometry : angle 0.54022 (38502) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 422 time to evaluate : 3.176 Fit side-chains REVERT: C 195 ASP cc_start: 0.7401 (p0) cc_final: 0.7096 (p0) REVERT: C 380 TYR cc_start: 0.8209 (t80) cc_final: 0.7848 (t80) REVERT: D 49 GLN cc_start: 0.8846 (pm20) cc_final: 0.8384 (pm20) REVERT: D 63 GLU cc_start: 0.7966 (tt0) cc_final: 0.7471 (tt0) REVERT: D 215 ASP cc_start: 0.7812 (m-30) cc_final: 0.7275 (m-30) REVERT: D 249 SER cc_start: 0.9081 (p) cc_final: 0.8834 (t) REVERT: E 20 VAL cc_start: 0.7392 (p) cc_final: 0.7156 (p) REVERT: E 36 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.8087 (ttp80) REVERT: E 211 ARG cc_start: 0.8243 (mpp80) cc_final: 0.7697 (mtt90) REVERT: E 316 MET cc_start: 0.6324 (mmm) cc_final: 0.5329 (ptt) REVERT: E 328 MET cc_start: 0.8560 (mtp) cc_final: 0.8265 (ttt) REVERT: F 1 MET cc_start: 0.4846 (ptt) cc_final: 0.4487 (ptm) REVERT: F 207 ASP cc_start: 0.8097 (m-30) cc_final: 0.7843 (m-30) REVERT: F 247 VAL cc_start: 0.9237 (p) cc_final: 0.8966 (m) REVERT: F 359 GLU cc_start: 0.4113 (mm-30) cc_final: 0.3145 (tt0) REVERT: F 364 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7467 (ttp-110) REVERT: H 163 MET cc_start: 0.8999 (ttt) cc_final: 0.8427 (ttt) REVERT: H 348 VAL cc_start: 0.7808 (p) cc_final: 0.7597 (t) REVERT: H 363 ASP cc_start: 0.8081 (p0) cc_final: 0.7865 (p0) REVERT: H 380 TYR cc_start: 0.8693 (t80) cc_final: 0.8380 (t80) REVERT: I 1 MET cc_start: -0.0283 (ptt) cc_final: -0.2505 (tpt) REVERT: I 215 ASP cc_start: 0.7782 (m-30) cc_final: 0.7521 (m-30) REVERT: I 220 ARG cc_start: 0.8653 (mtp85) cc_final: 0.8369 (mtp180) REVERT: I 232 ARG cc_start: 0.7996 (mmt90) cc_final: 0.6584 (mmp-170) REVERT: I 280 MET cc_start: 0.7784 (mtp) cc_final: 0.7396 (mtt) REVERT: A 101 ASP cc_start: 0.7581 (p0) cc_final: 0.7289 (p0) REVERT: A 135 LYS cc_start: 0.5174 (pptt) cc_final: 0.3980 (ttmm) REVERT: A 286 GLN cc_start: 0.8901 (mt0) cc_final: 0.8683 (mt0) REVERT: A 311 ASN cc_start: 0.7322 (m-40) cc_final: 0.7117 (m-40) REVERT: A 374 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8497 (ttp) REVERT: B 35 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7769 (mtmm) REVERT: B 298 MET cc_start: 0.9150 (tpt) cc_final: 0.8763 (tpt) REVERT: B 380 TYR cc_start: 0.8531 (t80) cc_final: 0.8206 (t80) REVERT: G 1 MET cc_start: 0.1147 (OUTLIER) cc_final: 0.0150 (tpt) REVERT: G 35 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8762 (mtmm) REVERT: G 211 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7028 (mmt-90) REVERT: G 215 ASP cc_start: 0.7598 (m-30) cc_final: 0.7225 (m-30) REVERT: G 239 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8610 (m) outliers start: 4 outliers final: 0 residues processed: 424 average time/residue: 0.3809 time to fit residues: 256.1181 Evaluate side-chains 324 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 321 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 142 optimal weight: 0.0980 chunk 275 optimal weight: 0.0370 chunk 106 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 overall best weight: 3.8264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 HIS E 18 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 49 GLN H 14 ASN H 18 ASN H 27 GLN H 120 ASN H 261 ASN H 317 HIS A 241 ASN A 281 HIS B 79 ASN G 27 GLN G 59 HIS G 120 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.090893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.077286 restraints weight = 49977.187| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.10 r_work: 0.2653 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 28458 Z= 0.215 Angle : 0.634 9.147 38502 Z= 0.339 Chirality : 0.048 0.168 4176 Planarity : 0.005 0.061 5040 Dihedral : 5.137 30.504 3940 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.74 % Favored : 90.15 % Rotamer: Outliers : 3.52 % Allowed : 19.73 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 3573 helix: 1.86 (0.23), residues: 601 sheet: -0.42 (0.20), residues: 628 loop : -2.51 (0.11), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 301 HIS 0.007 0.001 HIS F 317 PHE 0.015 0.002 PHE F 382 TYR 0.018 0.002 TYR E 96 ARG 0.007 0.000 ARG D 220 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 789) hydrogen bonds : angle 5.17605 ( 2313) covalent geometry : bond 0.00506 (28458) covalent geometry : angle 0.63411 (38502) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 310 time to evaluate : 2.919 Fit side-chains REVERT: C 76 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8936 (mtm180) REVERT: C 289 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8749 (mmm160) REVERT: D 49 GLN cc_start: 0.9097 (pm20) cc_final: 0.8608 (pm20) REVERT: D 63 GLU cc_start: 0.8670 (tt0) cc_final: 0.8248 (tt0) REVERT: D 163 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8755 (ttt) REVERT: D 215 ASP cc_start: 0.8466 (m-30) cc_final: 0.7987 (m-30) REVERT: D 217 ASP cc_start: 0.8134 (m-30) cc_final: 0.7634 (m-30) REVERT: D 399 LEU cc_start: 0.8529 (tt) cc_final: 0.8189 (tt) REVERT: E 317 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.8027 (m90) REVERT: F 1 MET cc_start: 0.4845 (ptt) cc_final: 0.4450 (ptm) REVERT: F 207 ASP cc_start: 0.8677 (m-30) cc_final: 0.8459 (m-30) REVERT: F 243 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8070 (ptp90) REVERT: F 317 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.7797 (m90) REVERT: F 364 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7819 (ttp-110) REVERT: H 163 MET cc_start: 0.9195 (ttt) cc_final: 0.8740 (ttt) REVERT: H 224 LYS cc_start: 0.9169 (mtmt) cc_final: 0.8969 (mttp) REVERT: H 228 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8835 (mt) REVERT: H 380 TYR cc_start: 0.8963 (t80) cc_final: 0.8669 (t80) REVERT: I 1 MET cc_start: 0.1325 (ptt) cc_final: -0.2612 (tpt) REVERT: I 232 ARG cc_start: 0.8388 (mmt90) cc_final: 0.6752 (mmp-170) REVERT: I 280 MET cc_start: 0.8204 (mtp) cc_final: 0.7813 (mtt) REVERT: I 351 LYS cc_start: 0.8479 (tttp) cc_final: 0.8123 (ttmt) REVERT: A 1 MET cc_start: 0.6044 (ttt) cc_final: 0.5224 (mmp) REVERT: A 101 ASP cc_start: 0.8061 (p0) cc_final: 0.7567 (p0) REVERT: A 135 LYS cc_start: 0.6469 (pptt) cc_final: 0.4625 (ttpt) REVERT: B 31 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8913 (ptt180) REVERT: B 334 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8501 (mp0) REVERT: B 380 TYR cc_start: 0.8857 (t80) cc_final: 0.8638 (t80) REVERT: B 385 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7271 (m-80) REVERT: G 1 MET cc_start: 0.1209 (mmt) cc_final: 0.0624 (tpp) REVERT: G 329 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9054 (tp) REVERT: G 371 MET cc_start: 0.8877 (mmm) cc_final: 0.8616 (mtt) outliers start: 103 outliers final: 54 residues processed: 394 average time/residue: 0.3561 time to fit residues: 225.7294 Evaluate side-chains 358 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 293 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 317 HIS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 317 HIS Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 258 MET Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 81 optimal weight: 8.9990 chunk 319 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 82 optimal weight: 0.0570 chunk 182 optimal weight: 0.0010 chunk 289 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 268 optimal weight: 0.3980 chunk 350 optimal weight: 7.9990 overall best weight: 1.0506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN H 311 ASN H 317 HIS I 300 HIS A 81 GLN A 281 HIS A 297 GLN A 317 HIS B 79 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.094447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.080831 restraints weight = 49696.196| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.10 r_work: 0.2714 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28458 Z= 0.111 Angle : 0.530 10.789 38502 Z= 0.284 Chirality : 0.045 0.151 4176 Planarity : 0.004 0.058 5040 Dihedral : 4.740 30.166 3933 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.73 % Favored : 91.16 % Rotamer: Outliers : 2.63 % Allowed : 20.62 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3573 helix: 2.14 (0.24), residues: 598 sheet: -0.22 (0.20), residues: 608 loop : -2.48 (0.11), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 378 HIS 0.023 0.001 HIS C 317 PHE 0.011 0.001 PHE B 382 TYR 0.014 0.001 TYR E 96 ARG 0.006 0.000 ARG D 220 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 789) hydrogen bonds : angle 4.85132 ( 2313) covalent geometry : bond 0.00222 (28458) covalent geometry : angle 0.53026 (38502) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 309 time to evaluate : 3.386 Fit side-chains revert: symmetry clash REVERT: C 76 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8810 (mtm180) REVERT: C 289 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8752 (mmm160) REVERT: C 380 TYR cc_start: 0.8680 (t80) cc_final: 0.8370 (t80) REVERT: D 49 GLN cc_start: 0.9046 (pm20) cc_final: 0.8561 (pm20) REVERT: D 63 GLU cc_start: 0.8603 (tt0) cc_final: 0.8174 (tt0) REVERT: D 163 MET cc_start: 0.8848 (ttp) cc_final: 0.8644 (ttt) REVERT: D 215 ASP cc_start: 0.8452 (m-30) cc_final: 0.7988 (m-30) REVERT: D 217 ASP cc_start: 0.8140 (m-30) cc_final: 0.7657 (m-30) REVERT: D 374 MET cc_start: 0.9073 (ttt) cc_final: 0.8838 (ttt) REVERT: D 399 LEU cc_start: 0.8355 (tt) cc_final: 0.8013 (tt) REVERT: E 20 VAL cc_start: 0.7554 (p) cc_final: 0.7306 (p) REVERT: E 211 ARG cc_start: 0.8791 (mpp80) cc_final: 0.8221 (mtt90) REVERT: E 271 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: F 1 MET cc_start: 0.4810 (ptt) cc_final: 0.4408 (ptm) REVERT: F 247 VAL cc_start: 0.9325 (p) cc_final: 0.8940 (m) REVERT: F 317 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.6673 (m90) REVERT: F 334 GLU cc_start: 0.8885 (pm20) cc_final: 0.8672 (pm20) REVERT: F 364 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7756 (ttp-110) REVERT: H 163 MET cc_start: 0.9189 (ttt) cc_final: 0.8737 (ttt) REVERT: H 228 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8780 (mt) REVERT: H 380 TYR cc_start: 0.8903 (t80) cc_final: 0.8602 (t80) REVERT: I 1 MET cc_start: 0.1133 (ptt) cc_final: -0.2655 (tpt) REVERT: I 232 ARG cc_start: 0.8348 (mmt90) cc_final: 0.6719 (mmp-170) REVERT: I 280 MET cc_start: 0.8202 (mtp) cc_final: 0.7808 (mtt) REVERT: A 101 ASP cc_start: 0.7886 (p0) cc_final: 0.7452 (p0) REVERT: A 135 LYS cc_start: 0.6466 (pptt) cc_final: 0.4783 (ttpt) REVERT: A 227 MET cc_start: 0.6275 (pmm) cc_final: 0.5532 (ptt) REVERT: B 109 MET cc_start: 0.9109 (mmt) cc_final: 0.8819 (mmt) REVERT: B 334 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: B 380 TYR cc_start: 0.8770 (t80) cc_final: 0.8543 (t80) REVERT: G 1 MET cc_start: 0.1256 (mmt) cc_final: 0.0663 (tpp) REVERT: G 256 GLU cc_start: 0.8314 (mp0) cc_final: 0.7959 (mp0) REVERT: G 329 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9012 (tp) outliers start: 77 outliers final: 45 residues processed: 371 average time/residue: 0.3525 time to fit residues: 213.2747 Evaluate side-chains 346 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 355 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 317 HIS Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 202 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 333 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 40 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 0.0670 chunk 127 optimal weight: 10.0000 overall best weight: 2.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN H 317 HIS A 281 HIS A 317 HIS B 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.092124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.078667 restraints weight = 50147.849| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.05 r_work: 0.2680 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 28458 Z= 0.159 Angle : 0.566 10.716 38502 Z= 0.302 Chirality : 0.046 0.174 4176 Planarity : 0.004 0.062 5040 Dihedral : 4.900 30.599 3933 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.54 % Favored : 90.37 % Rotamer: Outliers : 3.56 % Allowed : 19.86 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3573 helix: 2.13 (0.24), residues: 595 sheet: -0.30 (0.20), residues: 608 loop : -2.51 (0.11), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 301 HIS 0.007 0.001 HIS A 317 PHE 0.013 0.001 PHE F 382 TYR 0.017 0.001 TYR E 96 ARG 0.004 0.000 ARG I 398 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 789) hydrogen bonds : angle 4.86147 ( 2313) covalent geometry : bond 0.00366 (28458) covalent geometry : angle 0.56602 (38502) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 303 time to evaluate : 3.210 Fit side-chains REVERT: C 76 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8860 (mtm180) REVERT: C 247 VAL cc_start: 0.9461 (OUTLIER) cc_final: 0.9217 (t) REVERT: C 289 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8785 (mmm160) REVERT: C 380 TYR cc_start: 0.8764 (t80) cc_final: 0.8488 (t80) REVERT: D 49 GLN cc_start: 0.9060 (pm20) cc_final: 0.8590 (pm20) REVERT: D 63 GLU cc_start: 0.8635 (tt0) cc_final: 0.8206 (tt0) REVERT: D 163 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8713 (ttt) REVERT: D 215 ASP cc_start: 0.8453 (m-30) cc_final: 0.7949 (m-30) REVERT: D 217 ASP cc_start: 0.8257 (m-30) cc_final: 0.7737 (m-30) REVERT: D 399 LEU cc_start: 0.8427 (tt) cc_final: 0.8117 (tt) REVERT: E 20 VAL cc_start: 0.7598 (p) cc_final: 0.7328 (p) REVERT: E 211 ARG cc_start: 0.8814 (mpp80) cc_final: 0.8317 (mtt90) REVERT: F 1 MET cc_start: 0.4758 (ptt) cc_final: 0.4371 (ptm) REVERT: F 195 ASP cc_start: 0.8444 (m-30) cc_final: 0.8203 (t0) REVERT: F 317 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7300 (m90) REVERT: F 364 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7849 (ttp-110) REVERT: H 56 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8216 (ttt) REVERT: H 163 MET cc_start: 0.9173 (ttt) cc_final: 0.8726 (ttt) REVERT: H 380 TYR cc_start: 0.8945 (t80) cc_final: 0.8613 (t80) REVERT: I 1 MET cc_start: 0.0788 (ptt) cc_final: -0.3045 (tpt) REVERT: I 232 ARG cc_start: 0.8383 (mmt90) cc_final: 0.6758 (mmp-170) REVERT: I 280 MET cc_start: 0.8312 (mtp) cc_final: 0.7936 (mtt) REVERT: I 351 LYS cc_start: 0.8482 (tttp) cc_final: 0.8135 (ttmt) REVERT: A 101 ASP cc_start: 0.7999 (p0) cc_final: 0.7531 (p0) REVERT: A 135 LYS cc_start: 0.6495 (pptt) cc_final: 0.4800 (ttpt) REVERT: B 31 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8911 (ptt180) REVERT: B 109 MET cc_start: 0.9150 (mmt) cc_final: 0.8865 (mmt) REVERT: B 258 MET cc_start: 0.8922 (ttt) cc_final: 0.8617 (ttt) REVERT: B 380 TYR cc_start: 0.8845 (t80) cc_final: 0.8624 (t80) REVERT: B 385 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: G 1 MET cc_start: 0.1388 (mmt) cc_final: 0.0611 (tpp) REVERT: G 256 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: G 329 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9041 (tp) outliers start: 104 outliers final: 65 residues processed: 389 average time/residue: 0.3500 time to fit residues: 222.6856 Evaluate side-chains 368 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 293 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 385 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 317 HIS Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 72 optimal weight: 0.0470 chunk 207 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 260 optimal weight: 0.6980 chunk 328 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 297 optimal weight: 6.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN H 317 HIS A 281 HIS A 317 HIS B 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.093994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.080547 restraints weight = 49707.233| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.04 r_work: 0.2715 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28458 Z= 0.114 Angle : 0.531 14.513 38502 Z= 0.283 Chirality : 0.045 0.154 4176 Planarity : 0.004 0.059 5040 Dihedral : 4.727 29.965 3933 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.96 % Favored : 90.96 % Rotamer: Outliers : 3.49 % Allowed : 20.65 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3573 helix: 2.24 (0.24), residues: 594 sheet: -0.27 (0.20), residues: 638 loop : -2.46 (0.11), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 301 HIS 0.007 0.001 HIS A 317 PHE 0.009 0.001 PHE B 382 TYR 0.015 0.001 TYR E 96 ARG 0.006 0.000 ARG D 364 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 789) hydrogen bonds : angle 4.73587 ( 2313) covalent geometry : bond 0.00238 (28458) covalent geometry : angle 0.53113 (38502) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 299 time to evaluate : 3.355 Fit side-chains REVERT: C 76 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8766 (mtm180) REVERT: C 188 TYR cc_start: 0.9084 (m-80) cc_final: 0.8477 (m-80) REVERT: C 247 VAL cc_start: 0.9442 (OUTLIER) cc_final: 0.9195 (t) REVERT: C 289 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8777 (mmm160) REVERT: C 380 TYR cc_start: 0.8720 (t80) cc_final: 0.8441 (t80) REVERT: D 49 GLN cc_start: 0.9026 (pm20) cc_final: 0.8559 (pm20) REVERT: D 63 GLU cc_start: 0.8581 (tt0) cc_final: 0.8152 (tt0) REVERT: D 163 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8630 (ttt) REVERT: D 215 ASP cc_start: 0.8457 (m-30) cc_final: 0.7991 (m-30) REVERT: D 217 ASP cc_start: 0.8212 (m-30) cc_final: 0.7731 (m-30) REVERT: D 399 LEU cc_start: 0.8358 (tt) cc_final: 0.8058 (tt) REVERT: E 20 VAL cc_start: 0.7590 (p) cc_final: 0.7334 (p) REVERT: E 211 ARG cc_start: 0.8818 (mpp80) cc_final: 0.8323 (mtt90) REVERT: F 1 MET cc_start: 0.4751 (ptt) cc_final: 0.4338 (ptm) REVERT: F 195 ASP cc_start: 0.8426 (m-30) cc_final: 0.8196 (t0) REVERT: F 243 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8200 (ptp90) REVERT: F 247 VAL cc_start: 0.9321 (p) cc_final: 0.8957 (m) REVERT: F 317 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.6955 (m90) REVERT: F 363 ASP cc_start: 0.8672 (t70) cc_final: 0.8455 (t0) REVERT: F 364 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7694 (ttp-110) REVERT: H 56 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8146 (ttt) REVERT: H 162 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8307 (mm-30) REVERT: H 163 MET cc_start: 0.9172 (ttt) cc_final: 0.8737 (ttt) REVERT: H 380 TYR cc_start: 0.8915 (t80) cc_final: 0.8674 (t80) REVERT: I 1 MET cc_start: 0.0624 (ptt) cc_final: -0.3127 (tpt) REVERT: I 232 ARG cc_start: 0.8380 (mmt90) cc_final: 0.6819 (mmp-170) REVERT: I 280 MET cc_start: 0.8261 (mtp) cc_final: 0.7913 (mtt) REVERT: A 101 ASP cc_start: 0.7927 (p0) cc_final: 0.7490 (p0) REVERT: A 135 LYS cc_start: 0.6499 (pptt) cc_final: 0.4812 (ttpt) REVERT: A 280 MET cc_start: 0.7931 (tpt) cc_final: 0.7725 (tpt) REVERT: B 31 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.7297 (ptp-170) REVERT: B 109 MET cc_start: 0.9121 (mmt) cc_final: 0.8907 (mmt) REVERT: B 258 MET cc_start: 0.8866 (ttt) cc_final: 0.8610 (ttt) REVERT: B 380 TYR cc_start: 0.8802 (t80) cc_final: 0.8535 (t80) REVERT: B 385 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: G 1 MET cc_start: 0.1715 (mmt) cc_final: 0.0698 (tpp) REVERT: G 256 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: G 329 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9011 (tp) outliers start: 102 outliers final: 74 residues processed: 382 average time/residue: 0.3590 time to fit residues: 222.4801 Evaluate side-chains 378 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 293 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 385 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 243 ARG Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 317 HIS Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 317 HIS Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 201 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 312 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 340 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN A 281 HIS A 317 HIS B 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.092229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.078753 restraints weight = 50176.070| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.06 r_work: 0.2684 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 28458 Z= 0.158 Angle : 0.563 14.469 38502 Z= 0.300 Chirality : 0.046 0.147 4176 Planarity : 0.004 0.060 5040 Dihedral : 4.880 30.328 3933 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.63 % Favored : 90.29 % Rotamer: Outliers : 3.73 % Allowed : 20.34 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3573 helix: 2.17 (0.24), residues: 592 sheet: -0.30 (0.20), residues: 612 loop : -2.50 (0.11), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 301 HIS 0.019 0.001 HIS C 317 PHE 0.013 0.001 PHE F 382 TYR 0.017 0.001 TYR E 96 ARG 0.003 0.000 ARG D 220 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 789) hydrogen bonds : angle 4.79994 ( 2313) covalent geometry : bond 0.00365 (28458) covalent geometry : angle 0.56326 (38502) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 293 time to evaluate : 3.484 Fit side-chains REVERT: C 58 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8007 (ttpp) REVERT: C 247 VAL cc_start: 0.9450 (OUTLIER) cc_final: 0.9209 (t) REVERT: C 289 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8758 (mmm160) REVERT: C 317 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.8049 (m-70) REVERT: C 380 TYR cc_start: 0.8739 (t80) cc_final: 0.8426 (t80) REVERT: D 49 GLN cc_start: 0.9056 (pm20) cc_final: 0.8571 (pm20) REVERT: D 63 GLU cc_start: 0.8635 (tt0) cc_final: 0.8213 (tt0) REVERT: D 163 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8657 (ttt) REVERT: D 215 ASP cc_start: 0.8481 (m-30) cc_final: 0.8048 (m-30) REVERT: D 217 ASP cc_start: 0.8251 (m-30) cc_final: 0.7743 (m-30) REVERT: D 399 LEU cc_start: 0.8380 (tt) cc_final: 0.8107 (tt) REVERT: E 20 VAL cc_start: 0.7544 (p) cc_final: 0.7266 (p) REVERT: E 211 ARG cc_start: 0.8774 (mpp80) cc_final: 0.8277 (mtt90) REVERT: F 1 MET cc_start: 0.4663 (ptt) cc_final: 0.4249 (ptm) REVERT: F 195 ASP cc_start: 0.8492 (m-30) cc_final: 0.8290 (t0) REVERT: F 243 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8233 (ptp90) REVERT: F 247 VAL cc_start: 0.9324 (p) cc_final: 0.8961 (m) REVERT: F 317 HIS cc_start: 0.8246 (OUTLIER) cc_final: 0.7279 (m90) REVERT: F 363 ASP cc_start: 0.8624 (t70) cc_final: 0.8363 (t0) REVERT: F 364 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7724 (ttp-110) REVERT: H 56 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8205 (ttt) REVERT: H 162 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8260 (mm-30) REVERT: H 163 MET cc_start: 0.9125 (ttt) cc_final: 0.8657 (ttt) REVERT: H 380 TYR cc_start: 0.8944 (t80) cc_final: 0.8684 (t80) REVERT: I 1 MET cc_start: 0.0715 (ptt) cc_final: -0.3145 (tpt) REVERT: I 232 ARG cc_start: 0.8386 (mmt90) cc_final: 0.6787 (mmp-170) REVERT: I 280 MET cc_start: 0.8283 (mtp) cc_final: 0.7929 (mtt) REVERT: A 1 MET cc_start: 0.6268 (ttt) cc_final: 0.5199 (mmp) REVERT: A 101 ASP cc_start: 0.8025 (p0) cc_final: 0.7549 (p0) REVERT: A 135 LYS cc_start: 0.6467 (pptt) cc_final: 0.4736 (ttpt) REVERT: B 31 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.7396 (ptp-170) REVERT: B 109 MET cc_start: 0.9162 (mmt) cc_final: 0.8898 (mmt) REVERT: B 258 MET cc_start: 0.8923 (ttt) cc_final: 0.8593 (ttt) REVERT: B 380 TYR cc_start: 0.8838 (t80) cc_final: 0.8614 (t80) REVERT: B 385 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: G 1 MET cc_start: 0.1359 (mmt) cc_final: 0.0441 (tpp) REVERT: G 256 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: G 280 MET cc_start: 0.8439 (mtp) cc_final: 0.8198 (mtp) REVERT: G 329 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9037 (tp) outliers start: 109 outliers final: 78 residues processed: 383 average time/residue: 0.3669 time to fit residues: 229.1462 Evaluate side-chains 378 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 288 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 385 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 243 ARG Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 317 HIS Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 4 optimal weight: 0.0170 chunk 96 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN H 317 HIS A 281 HIS B 79 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.092215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.078740 restraints weight = 49965.485| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.06 r_work: 0.2685 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28458 Z= 0.148 Angle : 0.559 14.792 38502 Z= 0.297 Chirality : 0.046 0.166 4176 Planarity : 0.004 0.059 5040 Dihedral : 4.901 30.362 3933 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.52 % Favored : 90.40 % Rotamer: Outliers : 3.83 % Allowed : 20.58 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3573 helix: 2.19 (0.24), residues: 592 sheet: -0.30 (0.20), residues: 612 loop : -2.50 (0.11), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 301 HIS 0.013 0.001 HIS A 317 PHE 0.012 0.001 PHE F 382 TYR 0.017 0.001 TYR E 96 ARG 0.006 0.000 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 789) hydrogen bonds : angle 4.79692 ( 2313) covalent geometry : bond 0.00337 (28458) covalent geometry : angle 0.55939 (38502) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 295 time to evaluate : 2.993 Fit side-chains REVERT: C 58 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8079 (ttpp) REVERT: C 247 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9191 (t) REVERT: C 289 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8754 (mmm160) REVERT: C 317 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7629 (t70) REVERT: C 380 TYR cc_start: 0.8741 (t80) cc_final: 0.8471 (t80) REVERT: D 49 GLN cc_start: 0.9054 (pm20) cc_final: 0.8569 (pm20) REVERT: D 63 GLU cc_start: 0.8621 (tt0) cc_final: 0.8193 (tt0) REVERT: D 163 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8662 (ttt) REVERT: D 215 ASP cc_start: 0.8478 (m-30) cc_final: 0.8042 (m-30) REVERT: D 217 ASP cc_start: 0.8252 (m-30) cc_final: 0.7740 (m-30) REVERT: D 399 LEU cc_start: 0.8394 (tt) cc_final: 0.8146 (tt) REVERT: E 20 VAL cc_start: 0.7560 (p) cc_final: 0.7289 (p) REVERT: E 211 ARG cc_start: 0.8766 (mpp80) cc_final: 0.8268 (mtt90) REVERT: F 1 MET cc_start: 0.4850 (ptt) cc_final: 0.4403 (ptm) REVERT: F 195 ASP cc_start: 0.8478 (m-30) cc_final: 0.8277 (t0) REVERT: F 243 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8288 (ptp90) REVERT: F 247 VAL cc_start: 0.9327 (p) cc_final: 0.8956 (m) REVERT: F 317 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7266 (m90) REVERT: F 363 ASP cc_start: 0.8607 (t70) cc_final: 0.8389 (t0) REVERT: F 364 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7724 (ttp-110) REVERT: H 56 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8208 (ttt) REVERT: H 162 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8252 (mm-30) REVERT: H 163 MET cc_start: 0.9125 (ttt) cc_final: 0.8625 (ttt) REVERT: H 380 TYR cc_start: 0.8943 (t80) cc_final: 0.8686 (t80) REVERT: I 1 MET cc_start: 0.0683 (ptt) cc_final: -0.3188 (tpt) REVERT: I 232 ARG cc_start: 0.8386 (mmt90) cc_final: 0.6782 (mmp-170) REVERT: A 1 MET cc_start: 0.6271 (ttt) cc_final: 0.5194 (mmp) REVERT: A 101 ASP cc_start: 0.8026 (p0) cc_final: 0.7547 (p0) REVERT: A 135 LYS cc_start: 0.6459 (pptt) cc_final: 0.4723 (ttpt) REVERT: A 280 MET cc_start: 0.7963 (tpt) cc_final: 0.7649 (tpt) REVERT: B 31 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.6969 (ptp-170) REVERT: B 109 MET cc_start: 0.9173 (mmt) cc_final: 0.8925 (mmt) REVERT: B 258 MET cc_start: 0.8909 (ttt) cc_final: 0.8587 (ttt) REVERT: B 334 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8360 (pm20) REVERT: B 380 TYR cc_start: 0.8845 (t80) cc_final: 0.8615 (t80) REVERT: B 385 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: G 1 MET cc_start: 0.1460 (mmt) cc_final: 0.0321 (tpp) REVERT: G 256 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: G 280 MET cc_start: 0.8361 (mtp) cc_final: 0.8112 (mtp) REVERT: G 329 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9030 (tp) outliers start: 112 outliers final: 78 residues processed: 387 average time/residue: 0.3558 time to fit residues: 226.3557 Evaluate side-chains 380 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 289 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 194 SER Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 243 ARG Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 317 HIS Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 13 optimal weight: 4.9990 chunk 272 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 chunk 287 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 chunk 187 optimal weight: 0.3980 chunk 234 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 101 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 HIS D 94 ASN E 79 ASN F 49 GLN H 317 HIS A 49 GLN A 241 ASN A 281 HIS A 317 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.082845 restraints weight = 49761.161| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.04 r_work: 0.2753 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28458 Z= 0.102 Angle : 0.511 15.659 38502 Z= 0.271 Chirality : 0.044 0.153 4176 Planarity : 0.004 0.056 5040 Dihedral : 4.511 29.011 3933 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.90 % Favored : 91.02 % Rotamer: Outliers : 2.80 % Allowed : 21.61 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3573 helix: 2.18 (0.24), residues: 607 sheet: -0.24 (0.20), residues: 640 loop : -2.44 (0.11), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 378 HIS 0.021 0.001 HIS C 317 PHE 0.008 0.001 PHE C 382 TYR 0.014 0.001 TYR F 13 ARG 0.011 0.000 ARG C 398 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 789) hydrogen bonds : angle 4.56919 ( 2313) covalent geometry : bond 0.00199 (28458) covalent geometry : angle 0.51125 (38502) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 300 time to evaluate : 3.111 Fit side-chains REVERT: C 247 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9172 (t) REVERT: C 289 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8747 (mmm160) REVERT: C 380 TYR cc_start: 0.8608 (t80) cc_final: 0.8341 (t80) REVERT: D 49 GLN cc_start: 0.9009 (pm20) cc_final: 0.8550 (pm20) REVERT: D 63 GLU cc_start: 0.8535 (tt0) cc_final: 0.8118 (tt0) REVERT: D 163 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8590 (ttt) REVERT: D 215 ASP cc_start: 0.8501 (m-30) cc_final: 0.8088 (m-30) REVERT: D 217 ASP cc_start: 0.8214 (m-30) cc_final: 0.7678 (m-30) REVERT: D 399 LEU cc_start: 0.8366 (tt) cc_final: 0.8115 (tt) REVERT: E 211 ARG cc_start: 0.8784 (mpp80) cc_final: 0.8295 (mtt90) REVERT: F 1 MET cc_start: 0.4677 (ptt) cc_final: 0.4264 (ptm) REVERT: F 243 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7807 (ptp90) REVERT: F 247 VAL cc_start: 0.9301 (p) cc_final: 0.8940 (m) REVERT: F 317 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.6338 (m90) REVERT: F 364 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7807 (ttp-110) REVERT: H 162 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8278 (mm-30) REVERT: H 163 MET cc_start: 0.9133 (ttt) cc_final: 0.8683 (ttt) REVERT: H 380 TYR cc_start: 0.8880 (t80) cc_final: 0.8670 (t80) REVERT: I 1 MET cc_start: 0.0609 (ptt) cc_final: -0.3128 (tpt) REVERT: I 232 ARG cc_start: 0.8315 (mmt90) cc_final: 0.6683 (mmp-170) REVERT: A 101 ASP cc_start: 0.7952 (p0) cc_final: 0.7509 (p0) REVERT: A 135 LYS cc_start: 0.6468 (pptt) cc_final: 0.4804 (ttpt) REVERT: B 31 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.7406 (ptp-170) REVERT: B 334 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: B 380 TYR cc_start: 0.8750 (t80) cc_final: 0.8424 (t80) REVERT: G 1 MET cc_start: 0.1494 (mmt) cc_final: 0.0371 (tpp) REVERT: G 256 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: G 329 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8951 (tp) outliers start: 82 outliers final: 56 residues processed: 365 average time/residue: 0.3595 time to fit residues: 214.7993 Evaluate side-chains 355 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 290 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 243 ARG Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 317 HIS Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 235 optimal weight: 0.0270 chunk 221 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 161 optimal weight: 0.0870 chunk 165 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN F 49 GLN F 79 ASN H 317 HIS A 241 ASN A 281 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.094449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.080987 restraints weight = 50008.543| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.05 r_work: 0.2722 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28458 Z= 0.125 Angle : 0.535 14.961 38502 Z= 0.282 Chirality : 0.045 0.162 4176 Planarity : 0.004 0.055 5040 Dihedral : 4.599 29.084 3933 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.98 % Favored : 90.93 % Rotamer: Outliers : 2.67 % Allowed : 21.95 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3573 helix: 2.14 (0.24), residues: 607 sheet: -0.21 (0.20), residues: 638 loop : -2.43 (0.11), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 301 HIS 0.021 0.001 HIS A 317 PHE 0.010 0.001 PHE F 382 TYR 0.015 0.001 TYR E 96 ARG 0.004 0.000 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 789) hydrogen bonds : angle 4.61490 ( 2313) covalent geometry : bond 0.00278 (28458) covalent geometry : angle 0.53474 (38502) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 286 time to evaluate : 2.904 Fit side-chains REVERT: C 247 VAL cc_start: 0.9415 (OUTLIER) cc_final: 0.9176 (t) REVERT: C 289 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8742 (mmm160) REVERT: C 380 TYR cc_start: 0.8653 (t80) cc_final: 0.8396 (t80) REVERT: D 49 GLN cc_start: 0.9044 (pm20) cc_final: 0.8555 (pm20) REVERT: D 63 GLU cc_start: 0.8615 (tt0) cc_final: 0.8188 (tt0) REVERT: D 163 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8631 (ttt) REVERT: D 215 ASP cc_start: 0.8474 (m-30) cc_final: 0.8051 (m-30) REVERT: D 316 MET cc_start: 0.7877 (mmm) cc_final: 0.7640 (tpp) REVERT: D 399 LEU cc_start: 0.8395 (tt) cc_final: 0.8151 (tt) REVERT: E 211 ARG cc_start: 0.8773 (mpp80) cc_final: 0.8277 (mtt90) REVERT: F 1 MET cc_start: 0.4757 (ptt) cc_final: 0.4316 (ptm) REVERT: F 243 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7798 (ptp90) REVERT: F 247 VAL cc_start: 0.9313 (p) cc_final: 0.8935 (m) REVERT: F 317 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.6810 (m90) REVERT: H 56 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8146 (ttt) REVERT: H 162 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8242 (mm-30) REVERT: H 163 MET cc_start: 0.9128 (ttt) cc_final: 0.8668 (ttt) REVERT: H 380 TYR cc_start: 0.8888 (t80) cc_final: 0.8671 (t80) REVERT: I 1 MET cc_start: 0.0273 (ptt) cc_final: -0.3659 (tpt) REVERT: I 232 ARG cc_start: 0.8368 (mmt90) cc_final: 0.6752 (mmp-170) REVERT: A 1 MET cc_start: 0.6016 (ttt) cc_final: 0.5178 (mmp) REVERT: A 101 ASP cc_start: 0.7982 (p0) cc_final: 0.7538 (p0) REVERT: A 135 LYS cc_start: 0.6408 (pptt) cc_final: 0.4648 (ttpt) REVERT: B 31 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7272 (ptp-170) REVERT: B 84 ASP cc_start: 0.7952 (t0) cc_final: 0.7461 (p0) REVERT: B 258 MET cc_start: 0.8888 (ttt) cc_final: 0.8658 (ttt) REVERT: B 334 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8211 (pm20) REVERT: B 380 TYR cc_start: 0.8792 (t80) cc_final: 0.8502 (t80) REVERT: G 1 MET cc_start: 0.1694 (mmt) cc_final: 0.1081 (mtm) REVERT: G 256 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: G 329 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8984 (tp) outliers start: 78 outliers final: 60 residues processed: 349 average time/residue: 0.3454 time to fit residues: 197.5516 Evaluate side-chains 354 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 284 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 317 HIS Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 243 ARG Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 317 HIS Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 1 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN A 241 ASN A 317 HIS G 158 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.088665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.075277 restraints weight = 50492.082| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.05 r_work: 0.2623 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 28458 Z= 0.294 Angle : 0.700 15.496 38502 Z= 0.372 Chirality : 0.051 0.175 4176 Planarity : 0.005 0.061 5040 Dihedral : 5.535 31.751 3933 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.72 % Favored : 89.17 % Rotamer: Outliers : 2.94 % Allowed : 21.40 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 3573 helix: 1.79 (0.23), residues: 595 sheet: -0.29 (0.20), residues: 618 loop : -2.61 (0.11), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 389 HIS 0.008 0.002 HIS A 317 PHE 0.020 0.002 PHE F 382 TYR 0.024 0.002 TYR E 96 ARG 0.006 0.001 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 789) hydrogen bonds : angle 5.13338 ( 2313) covalent geometry : bond 0.00714 (28458) covalent geometry : angle 0.69996 (38502) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7146 Ramachandran restraints generated. 3573 Oldfield, 0 Emsley, 3573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 277 time to evaluate : 2.923 Fit side-chains revert: symmetry clash REVERT: C 247 VAL cc_start: 0.9469 (OUTLIER) cc_final: 0.9218 (t) REVERT: C 289 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8774 (mmm160) REVERT: C 309 ASP cc_start: 0.8121 (t0) cc_final: 0.7816 (t0) REVERT: D 49 GLN cc_start: 0.9090 (pm20) cc_final: 0.8594 (pm20) REVERT: D 63 GLU cc_start: 0.8671 (tt0) cc_final: 0.8288 (tt0) REVERT: D 163 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8885 (ttt) REVERT: D 215 ASP cc_start: 0.8453 (m-30) cc_final: 0.8028 (m-30) REVERT: F 1 MET cc_start: 0.4643 (ptt) cc_final: 0.4218 (ptm) REVERT: F 109 MET cc_start: 0.9433 (mmt) cc_final: 0.9049 (mmt) REVERT: H 56 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8316 (ttt) REVERT: H 163 MET cc_start: 0.9166 (ttt) cc_final: 0.8676 (ttt) REVERT: H 380 TYR cc_start: 0.8960 (t80) cc_final: 0.8653 (t80) REVERT: I 1 MET cc_start: 0.0740 (ptt) cc_final: 0.0408 (ptt) REVERT: I 232 ARG cc_start: 0.8447 (mmt90) cc_final: 0.6782 (mmp-170) REVERT: I 351 LYS cc_start: 0.8575 (tttp) cc_final: 0.8207 (ttmt) REVERT: A 1 MET cc_start: 0.6295 (ttt) cc_final: 0.5235 (mmp) REVERT: A 101 ASP cc_start: 0.8285 (p0) cc_final: 0.7840 (p0) REVERT: A 135 LYS cc_start: 0.6562 (pptt) cc_final: 0.4842 (ttpt) REVERT: A 280 MET cc_start: 0.8039 (tpt) cc_final: 0.7732 (tpt) REVERT: B 31 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.6919 (ptp-170) REVERT: B 385 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: G 1 MET cc_start: 0.1705 (mmt) cc_final: 0.1417 (mtm) REVERT: G 256 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: G 329 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9127 (tp) outliers start: 86 outliers final: 62 residues processed: 349 average time/residue: 0.3434 time to fit residues: 197.1458 Evaluate side-chains 342 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 243 ARG Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 243 ARG Chi-restraints excluded: chain H residue 247 VAL Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain I residue 317 HIS Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 256 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 85 optimal weight: 0.7980 chunk 329 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 233 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN H 317 HIS A 241 ASN A 281 HIS A 317 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.081408 restraints weight = 50027.141| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.11 r_work: 0.2725 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28458 Z= 0.111 Angle : 0.540 17.515 38502 Z= 0.286 Chirality : 0.045 0.156 4176 Planarity : 0.004 0.057 5040 Dihedral : 4.795 30.532 3933 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.59 % Favored : 91.32 % Rotamer: Outliers : 2.19 % Allowed : 22.29 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 3573 helix: 1.91 (0.23), residues: 616 sheet: -0.34 (0.20), residues: 584 loop : -2.51 (0.11), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 378 HIS 0.006 0.001 HIS D 317 PHE 0.009 0.001 PHE C 382 TYR 0.015 0.001 TYR E 96 ARG 0.004 0.000 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 789) hydrogen bonds : angle 4.71235 ( 2313) covalent geometry : bond 0.00225 (28458) covalent geometry : angle 0.54047 (38502) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19101.48 seconds wall clock time: 331 minutes 40.44 seconds (19900.44 seconds total)