Starting phenix.real_space_refine on Mon Aug 25 11:37:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgn_44518/08_2025/9bgn_44518.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgn_44518/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bgn_44518/08_2025/9bgn_44518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgn_44518/08_2025/9bgn_44518.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bgn_44518/08_2025/9bgn_44518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgn_44518/08_2025/9bgn_44518.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.84, per 1000 atoms: 0.25 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: 2.37 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.17 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: 5.56 Time building geometry restraints manager: 3.16 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: 0.01 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: 10.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.420 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- 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 : 5.06 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 232 TYR 0.016 0.001 TYR E 96 PHE 0.010 0.001 PHE C 373 TRP 0.008 0.001 TRP B 378 HIS 0.009 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00238 (28458) covalent geometry : angle 0.54022 (38502) hydrogen bonds : bond 0.15899 ( 789) hydrogen bonds : angle 6.07670 ( 2313) *********************** 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 : 1.191 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: 0.1930 time to fit residues: 129.9521 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 : 1.326 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.091314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.077692 restraints weight = 50097.369| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.10 r_work: 0.2660 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 28458 Z= 0.203 Angle : 0.623 8.954 38502 Z= 0.333 Chirality : 0.048 0.193 4176 Planarity : 0.005 0.061 5040 Dihedral : 5.072 30.502 3940 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.60 % Favored : 90.29 % Rotamer: Outliers : 3.32 % Allowed : 19.86 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.14), residues: 3573 helix: 1.88 (0.23), residues: 601 sheet: -0.41 (0.20), residues: 628 loop : -2.51 (0.11), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 220 TYR 0.017 0.002 TYR E 96 PHE 0.014 0.002 PHE F 382 TRP 0.006 0.001 TRP I 301 HIS 0.007 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00479 (28458) covalent geometry : angle 0.62307 (38502) hydrogen bonds : bond 0.04944 ( 789) hydrogen bonds : angle 5.15635 ( 2313) *********************** 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 408 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 311 time to evaluate : 0.844 Fit side-chains REVERT: C 76 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8936 (mtm180) REVERT: C 289 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8741 (mmm160) REVERT: D 49 GLN cc_start: 0.9092 (pm20) cc_final: 0.8607 (pm20) REVERT: D 63 GLU cc_start: 0.8674 (tt0) cc_final: 0.8255 (tt0) REVERT: D 163 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8718 (ttt) REVERT: D 215 ASP cc_start: 0.8461 (m-30) cc_final: 0.7985 (m-30) REVERT: D 217 ASP cc_start: 0.8123 (m-30) cc_final: 0.7623 (m-30) REVERT: D 399 LEU cc_start: 0.8517 (tt) cc_final: 0.8178 (tt) REVERT: E 20 VAL cc_start: 0.7687 (p) cc_final: 0.7438 (p) REVERT: E 317 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.8040 (m90) REVERT: F 1 MET cc_start: 0.4853 (ptt) cc_final: 0.4462 (ptm) REVERT: F 207 ASP cc_start: 0.8675 (m-30) cc_final: 0.8461 (m-30) REVERT: F 316 MET cc_start: 0.8504 (mmp) cc_final: 0.8185 (mmp) REVERT: F 317 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7691 (m90) REVERT: F 364 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7811 (ttp-110) REVERT: H 163 MET cc_start: 0.9193 (ttt) cc_final: 0.8747 (ttt) REVERT: H 224 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8960 (mttp) REVERT: H 228 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8807 (mt) REVERT: H 380 TYR cc_start: 0.8960 (t80) cc_final: 0.8623 (t80) REVERT: I 1 MET cc_start: 0.1298 (ptt) cc_final: -0.2589 (tpt) REVERT: I 232 ARG cc_start: 0.8385 (mmt90) cc_final: 0.6753 (mmp-170) REVERT: I 280 MET cc_start: 0.8228 (mtp) cc_final: 0.7829 (mtt) REVERT: I 351 LYS cc_start: 0.8474 (tttp) cc_final: 0.8105 (ttmt) REVERT: A 1 MET cc_start: 0.6043 (ttt) cc_final: 0.5220 (mmp) REVERT: A 101 ASP cc_start: 0.8078 (p0) cc_final: 0.7573 (p0) REVERT: A 135 LYS cc_start: 0.6468 (pptt) cc_final: 0.4632 (ttpt) REVERT: B 31 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8908 (ptt180) REVERT: B 334 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: B 380 TYR cc_start: 0.8851 (t80) cc_final: 0.8628 (t80) REVERT: G 1 MET cc_start: 0.1104 (mmt) cc_final: 0.0463 (tpp) REVERT: G 215 ASP cc_start: 0.8283 (m-30) cc_final: 0.7984 (m-30) REVERT: G 316 MET cc_start: 0.8521 (mmt) cc_final: 0.8304 (mmt) REVERT: G 329 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9048 (tp) REVERT: G 371 MET cc_start: 0.8879 (mmm) cc_final: 0.8604 (mtt) outliers start: 97 outliers final: 49 residues processed: 389 average time/residue: 0.1491 time to fit residues: 94.8303 Evaluate side-chains 355 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 297 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 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 194 SER Chi-restraints excluded: chain F residue 239 VAL 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 334 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain G residue 50 LEU 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 59 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 136 optimal weight: 0.0030 chunk 218 optimal weight: 5.9990 chunk 304 optimal weight: 7.9990 chunk 242 optimal weight: 0.2980 chunk 210 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 overall best weight: 3.0596 ------------------------------------------------------------------------------- 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 261 ASN H 311 ASN H 317 HIS A 281 HIS A 297 GLN B 79 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.091146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.077503 restraints weight = 50451.204| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.12 r_work: 0.2660 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 28458 Z= 0.176 Angle : 0.589 10.854 38502 Z= 0.316 Chirality : 0.047 0.150 4176 Planarity : 0.004 0.060 5040 Dihedral : 5.091 30.631 3933 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.54 % Favored : 90.34 % Rotamer: Outliers : 3.56 % Allowed : 19.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.13), residues: 3573 helix: 1.95 (0.24), residues: 598 sheet: -0.33 (0.20), residues: 608 loop : -2.55 (0.11), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 220 TYR 0.018 0.001 TYR E 96 PHE 0.013 0.001 PHE F 382 TRP 0.006 0.001 TRP I 301 HIS 0.020 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00408 (28458) covalent geometry : angle 0.58923 (38502) hydrogen bonds : bond 0.04542 ( 789) hydrogen bonds : angle 5.03177 ( 2313) *********************** 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 405 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 301 time to evaluate : 1.051 Fit side-chains REVERT: C 58 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8174 (ttpp) REVERT: C 76 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8864 (mtm180) REVERT: C 289 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8777 (mmm160) REVERT: D 49 GLN cc_start: 0.9089 (pm20) cc_final: 0.8595 (pm20) REVERT: D 63 GLU cc_start: 0.8663 (tt0) cc_final: 0.8306 (tt0) REVERT: D 215 ASP cc_start: 0.8452 (m-30) cc_final: 0.7945 (m-30) REVERT: D 217 ASP cc_start: 0.8209 (m-30) cc_final: 0.7748 (m-30) REVERT: D 374 MET cc_start: 0.9127 (ttt) cc_final: 0.8846 (ttt) REVERT: D 399 LEU cc_start: 0.8509 (tt) cc_final: 0.8179 (tt) REVERT: F 1 MET cc_start: 0.4829 (ptt) cc_final: 0.4433 (ptm) REVERT: F 195 ASP cc_start: 0.8495 (m-30) cc_final: 0.8238 (t0) REVERT: F 316 MET cc_start: 0.8681 (mmp) cc_final: 0.8433 (mmp) REVERT: F 317 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.7530 (m90) REVERT: F 334 GLU cc_start: 0.8950 (pm20) cc_final: 0.8716 (pm20) REVERT: F 364 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7921 (ttp-110) REVERT: H 163 MET cc_start: 0.9191 (ttt) cc_final: 0.8732 (ttt) REVERT: H 228 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8836 (mt) REVERT: H 380 TYR cc_start: 0.8960 (t80) cc_final: 0.8644 (t80) REVERT: I 1 MET cc_start: 0.0857 (ptt) cc_final: -0.2970 (tpt) REVERT: I 232 ARG cc_start: 0.8385 (mmt90) cc_final: 0.6743 (mmp-170) REVERT: I 280 MET cc_start: 0.8356 (mtp) cc_final: 0.7987 (mtt) REVERT: A 1 MET cc_start: 0.6268 (ttt) cc_final: 0.5211 (mmp) REVERT: A 101 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7597 (p0) REVERT: A 135 LYS cc_start: 0.6497 (pptt) cc_final: 0.4632 (ttpt) REVERT: A 227 MET cc_start: 0.6262 (pmm) cc_final: 0.5534 (ptt) REVERT: B 31 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.7348 (ptp-170) REVERT: B 334 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: B 380 TYR cc_start: 0.8866 (t80) cc_final: 0.8646 (t80) REVERT: B 385 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: G 1 MET cc_start: 0.1236 (mmt) cc_final: 0.0453 (tpp) REVERT: G 256 GLU cc_start: 0.8320 (mp0) cc_final: 0.7929 (mp0) REVERT: G 329 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9076 (tp) REVERT: G 371 MET cc_start: 0.8876 (mmm) cc_final: 0.8665 (mtt) outliers start: 104 outliers final: 67 residues processed: 383 average time/residue: 0.1532 time to fit residues: 95.8624 Evaluate side-chains 365 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 288 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 155 MET 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 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 129 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 145 GLU 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 318 GLU 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 205 THR Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 314 VAL 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 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 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 H residue 363 ASP 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 331 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 101 ASP 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 317 HIS Chi-restraints excluded: chain B residue 334 GLU 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 151 SER Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 258 MET 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 309 optimal weight: 0.0030 chunk 348 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 240 optimal weight: 0.0030 chunk 256 optimal weight: 6.9990 chunk 62 optimal weight: 0.0470 chunk 59 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 276 optimal weight: 0.0770 overall best weight: 0.2056 ------------------------------------------------------------------------------- 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 311 ASN H 317 HIS A 49 GLN A 281 HIS A 317 HIS B 79 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.084326 restraints weight = 49805.493| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.11 r_work: 0.2775 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1324 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= 0.098 Angle : 0.508 12.293 38502 Z= 0.270 Chirality : 0.044 0.140 4176 Planarity : 0.004 0.053 5040 Dihedral : 4.432 28.191 3933 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.56 % Favored : 91.32 % Rotamer: Outliers : 2.67 % Allowed : 20.99 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.14), residues: 3573 helix: 2.26 (0.24), residues: 595 sheet: -0.18 (0.20), residues: 615 loop : -2.44 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 220 TYR 0.015 0.001 TYR F 13 PHE 0.008 0.001 PHE G 267 TRP 0.007 0.001 TRP F 301 HIS 0.007 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00190 (28458) covalent geometry : angle 0.50760 (38502) hydrogen bonds : bond 0.02753 ( 789) hydrogen bonds : angle 4.58978 ( 2313) *********************** 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 411 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 333 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: C 94 ASN cc_start: 0.8479 (m-40) cc_final: 0.8231 (m-40) REVERT: C 188 TYR cc_start: 0.9042 (m-80) cc_final: 0.8393 (m-80) REVERT: C 247 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9207 (t) REVERT: D 49 GLN cc_start: 0.9009 (pm20) cc_final: 0.8549 (pm20) REVERT: D 63 GLU cc_start: 0.8579 (tt0) cc_final: 0.8172 (tt0) REVERT: D 215 ASP cc_start: 0.8485 (m-30) cc_final: 0.8005 (m-30) REVERT: D 217 ASP cc_start: 0.8067 (m-30) cc_final: 0.7618 (m-30) REVERT: D 399 LEU cc_start: 0.8390 (tt) cc_final: 0.8121 (tt) REVERT: E 211 ARG cc_start: 0.8743 (mpp80) cc_final: 0.8243 (mtt90) REVERT: E 271 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: F 1 MET cc_start: 0.4822 (ptt) cc_final: 0.4449 (ptm) REVERT: F 233 MET cc_start: 0.9208 (mmp) cc_final: 0.8927 (mmp) REVERT: F 247 VAL cc_start: 0.9286 (p) cc_final: 0.8951 (m) REVERT: F 317 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.5655 (m90) REVERT: F 334 GLU cc_start: 0.8764 (pm20) cc_final: 0.8524 (pm20) REVERT: F 364 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7692 (ttp-110) REVERT: H 56 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8106 (ttt) REVERT: H 162 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8294 (mm-30) REVERT: H 163 MET cc_start: 0.9147 (ttt) cc_final: 0.8707 (ttt) REVERT: H 228 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8741 (mt) REVERT: H 311 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6745 (p0) REVERT: H 380 TYR cc_start: 0.8871 (t80) cc_final: 0.8670 (t80) REVERT: I 1 MET cc_start: 0.1158 (ptt) cc_final: -0.2646 (tpt) REVERT: I 232 ARG cc_start: 0.8274 (mmt90) cc_final: 0.6642 (mmp-170) REVERT: I 280 MET cc_start: 0.8035 (mtp) cc_final: 0.7685 (mtt) REVERT: I 383 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8733 (ttt) REVERT: A 101 ASP cc_start: 0.7821 (p0) cc_final: 0.7448 (p0) REVERT: A 135 LYS cc_start: 0.6620 (pptt) cc_final: 0.4840 (ttpt) REVERT: A 227 MET cc_start: 0.6184 (pmm) cc_final: 0.5890 (ptt) REVERT: B 109 MET cc_start: 0.9088 (mmt) cc_final: 0.8881 (mmt) REVERT: B 380 TYR cc_start: 0.8673 (t80) cc_final: 0.8379 (t80) REVERT: G 1 MET cc_start: 0.1594 (mmt) cc_final: 0.0646 (tpp) REVERT: G 256 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: G 329 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8936 (tp) outliers start: 78 outliers final: 36 residues processed: 392 average time/residue: 0.1391 time to fit residues: 90.7877 Evaluate side-chains 353 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 308 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain D residue 83 ILE 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 119 VAL Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 317 HIS 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 239 VAL 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 311 ASN 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 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 383 MET 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 314 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 384 VAL 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 170 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 ASN F 49 GLN A 241 ASN B 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.081835 restraints weight = 50055.615| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.06 r_work: 0.2738 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28458 Z= 0.120 Angle : 0.524 13.253 38502 Z= 0.278 Chirality : 0.045 0.185 4176 Planarity : 0.004 0.057 5040 Dihedral : 4.494 28.463 3933 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.76 % Favored : 91.16 % Rotamer: Outliers : 2.80 % Allowed : 20.68 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.14), residues: 3573 helix: 2.31 (0.24), residues: 594 sheet: -0.13 (0.20), residues: 620 loop : -2.41 (0.11), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 398 TYR 0.016 0.001 TYR E 96 PHE 0.010 0.001 PHE B 382 TRP 0.006 0.001 TRP I 301 HIS 0.015 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00262 (28458) covalent geometry : angle 0.52449 (38502) hydrogen bonds : bond 0.03260 ( 789) hydrogen bonds : angle 4.59221 ( 2313) *********************** 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 384 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 302 time to evaluate : 1.085 Fit side-chains REVERT: C 76 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8773 (mtm180) REVERT: C 247 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9205 (t) REVERT: C 289 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8781 (mmm160) REVERT: D 49 GLN cc_start: 0.9033 (pm20) cc_final: 0.8568 (pm20) REVERT: D 63 GLU cc_start: 0.8560 (tt0) cc_final: 0.8143 (tt0) REVERT: D 215 ASP cc_start: 0.8495 (m-30) cc_final: 0.8045 (m-30) REVERT: D 217 ASP cc_start: 0.8190 (m-30) cc_final: 0.7780 (m-30) REVERT: D 399 LEU cc_start: 0.8357 (tt) cc_final: 0.8065 (tt) REVERT: E 20 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7159 (p) REVERT: E 211 ARG cc_start: 0.8793 (mpp80) cc_final: 0.8306 (mtt90) REVERT: F 1 MET cc_start: 0.4715 (ptt) cc_final: 0.4326 (ptm) REVERT: F 247 VAL cc_start: 0.9314 (p) cc_final: 0.8958 (m) REVERT: F 316 MET cc_start: 0.8496 (mmp) cc_final: 0.8171 (mmp) REVERT: F 317 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.6378 (m90) REVERT: F 364 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7752 (ttp-110) REVERT: H 56 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8106 (ttt) REVERT: H 162 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8313 (mm-30) REVERT: H 163 MET cc_start: 0.9140 (ttt) cc_final: 0.8692 (ttt) REVERT: H 380 TYR cc_start: 0.8893 (t80) cc_final: 0.8679 (t80) REVERT: I 1 MET cc_start: 0.1169 (ptt) cc_final: -0.2833 (tpt) REVERT: I 232 ARG cc_start: 0.8359 (mmt90) cc_final: 0.6765 (mmp-170) REVERT: I 280 MET cc_start: 0.8033 (mtp) cc_final: 0.7714 (mtt) REVERT: A 1 MET cc_start: 0.6137 (ttt) cc_final: 0.5204 (mmp) REVERT: A 101 ASP cc_start: 0.7979 (p0) cc_final: 0.7576 (p0) REVERT: A 135 LYS cc_start: 0.6468 (pptt) cc_final: 0.4840 (ttpt) REVERT: A 317 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.8088 (t-90) REVERT: B 109 MET cc_start: 0.9114 (mmt) cc_final: 0.8914 (mmt) REVERT: B 280 MET cc_start: 0.7109 (mtp) cc_final: 0.6821 (mtm) REVERT: B 380 TYR cc_start: 0.8771 (t80) cc_final: 0.8490 (t80) REVERT: G 1 MET cc_start: 0.1468 (mmt) cc_final: 0.0560 (tpp) REVERT: G 256 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: G 329 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8974 (tp) outliers start: 82 outliers final: 52 residues processed: 371 average time/residue: 0.1503 time to fit residues: 92.0932 Evaluate side-chains 355 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 314 VAL Chi-restraints excluded: chain C residue 324 SER 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 204 VAL Chi-restraints excluded: chain D residue 317 HIS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 119 VAL 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 239 VAL 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 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 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 129 ILE 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 374 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 0 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 F 49 GLN H 317 HIS A 241 ASN A 281 HIS B 79 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.094865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.081409 restraints weight = 49899.483| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.05 r_work: 0.2731 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28458 Z= 0.119 Angle : 0.525 13.041 38502 Z= 0.279 Chirality : 0.045 0.156 4176 Planarity : 0.004 0.055 5040 Dihedral : 4.548 28.403 3933 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.84 % Favored : 91.07 % Rotamer: Outliers : 3.38 % Allowed : 20.31 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.14), residues: 3573 helix: 2.31 (0.24), residues: 594 sheet: -0.20 (0.20), residues: 638 loop : -2.40 (0.11), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 220 TYR 0.016 0.001 TYR E 96 PHE 0.010 0.001 PHE F 382 TRP 0.006 0.001 TRP I 301 HIS 0.004 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00258 (28458) covalent geometry : angle 0.52514 (38502) hydrogen bonds : bond 0.03327 ( 789) hydrogen bonds : angle 4.61077 ( 2313) *********************** 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 397 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 298 time to evaluate : 0.913 Fit side-chains REVERT: C 76 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8769 (mtm180) REVERT: C 247 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9187 (t) REVERT: C 289 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8745 (mmm160) REVERT: D 49 GLN cc_start: 0.9043 (pm20) cc_final: 0.8567 (pm20) REVERT: D 63 GLU cc_start: 0.8576 (tt0) cc_final: 0.8153 (tt0) REVERT: D 215 ASP cc_start: 0.8480 (m-30) cc_final: 0.8001 (m-30) REVERT: D 217 ASP cc_start: 0.8212 (m-30) cc_final: 0.7814 (m-30) REVERT: D 399 LEU cc_start: 0.8268 (tt) cc_final: 0.7994 (tt) REVERT: E 20 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7161 (p) REVERT: E 211 ARG cc_start: 0.8765 (mpp80) cc_final: 0.8268 (mtt90) REVERT: F 1 MET cc_start: 0.4679 (ptt) cc_final: 0.4285 (ptm) REVERT: F 81 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7094 (mm-40) REVERT: F 243 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7592 (ptp90) REVERT: F 247 VAL cc_start: 0.9312 (p) cc_final: 0.8964 (m) REVERT: F 316 MET cc_start: 0.8592 (mmp) cc_final: 0.8291 (mmp) REVERT: F 317 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.6730 (m90) REVERT: F 364 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7721 (ttp-110) REVERT: H 56 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8127 (ttt) REVERT: H 162 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8243 (mm-30) REVERT: H 163 MET cc_start: 0.9128 (ttt) cc_final: 0.8696 (ttt) REVERT: H 380 TYR cc_start: 0.8874 (t80) cc_final: 0.8650 (t80) REVERT: I 1 MET cc_start: 0.0513 (ptt) cc_final: -0.3162 (tpt) REVERT: I 232 ARG cc_start: 0.8340 (mmt90) cc_final: 0.6718 (mmp-170) REVERT: I 280 MET cc_start: 0.8004 (mtp) cc_final: 0.7676 (mtt) REVERT: A 101 ASP cc_start: 0.7993 (p0) cc_final: 0.7571 (p0) REVERT: A 135 LYS cc_start: 0.6404 (pptt) cc_final: 0.4750 (ttpt) REVERT: A 280 MET cc_start: 0.7931 (tpt) cc_final: 0.7705 (tpt) REVERT: B 31 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8835 (ptt180) REVERT: B 280 MET cc_start: 0.7014 (mtp) cc_final: 0.6722 (mtm) REVERT: B 380 TYR cc_start: 0.8775 (t80) cc_final: 0.8488 (t80) REVERT: B 385 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: G 1 MET cc_start: 0.1324 (mmt) cc_final: 0.0418 (tpp) REVERT: G 256 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: G 329 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8971 (tp) outliers start: 99 outliers final: 65 residues processed: 382 average time/residue: 0.1431 time to fit residues: 90.2101 Evaluate side-chains 369 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 ARG 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 385 PHE 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 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 20 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 119 VAL 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 81 GLN Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 194 SER 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 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 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 31 ARG 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 204 VAL 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 371 MET Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 385 PHE 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.76 > 50: distance: 36 - 212: 36.845 distance: 39 - 209: 31.744 distance: 135 - 152: 35.112 distance: 137 - 141: 24.580 distance: 138 - 149: 19.277 distance: 141 - 142: 37.131 distance: 142 - 143: 25.735 distance: 143 - 144: 29.009 distance: 143 - 145: 36.317 distance: 145 - 146: 19.176 distance: 146 - 147: 6.267 distance: 147 - 148: 36.157 distance: 147 - 149: 26.931 distance: 149 - 150: 28.805 distance: 150 - 151: 22.635 distance: 150 - 153: 3.063 distance: 151 - 152: 41.339 distance: 151 - 158: 22.194 distance: 153 - 154: 27.407 distance: 154 - 155: 7.843 distance: 155 - 156: 26.069 distance: 156 - 157: 4.226 distance: 158 - 159: 22.620 distance: 159 - 160: 8.612 distance: 159 - 162: 10.775 distance: 160 - 170: 6.806 distance: 162 - 163: 15.240 distance: 163 - 164: 5.629 distance: 163 - 165: 7.258 distance: 164 - 166: 9.762 distance: 165 - 167: 3.951 distance: 166 - 168: 6.195 distance: 167 - 168: 4.743 distance: 168 - 169: 4.587 distance: 170 - 171: 38.551 distance: 171 - 172: 24.720 distance: 171 - 174: 30.693 distance: 172 - 173: 13.567 distance: 172 - 176: 35.891 distance: 174 - 175: 19.007 distance: 176 - 177: 26.534 distance: 177 - 178: 40.338 distance: 177 - 180: 40.558 distance: 178 - 183: 26.165 distance: 180 - 181: 15.007 distance: 180 - 182: 26.638 distance: 183 - 184: 34.298 distance: 183 - 253: 31.774 distance: 184 - 185: 25.027 distance: 184 - 187: 55.504 distance: 185 - 186: 57.549 distance: 185 - 194: 54.425 distance: 186 - 250: 33.443 distance: 187 - 188: 38.900 distance: 188 - 189: 21.536 distance: 188 - 190: 25.173 distance: 189 - 191: 34.895 distance: 190 - 192: 22.093 distance: 191 - 193: 21.267 distance: 192 - 193: 33.298 distance: 194 - 195: 13.855 distance: 194 - 200: 17.509 distance: 195 - 196: 22.506 distance: 195 - 198: 7.352 distance: 196 - 197: 18.812 distance: 196 - 201: 54.331 distance: 198 - 199: 26.560 distance: 199 - 200: 36.802 distance: 201 - 202: 37.037 distance: 201 - 239: 38.202 distance: 202 - 203: 28.969 distance: 202 - 205: 26.053 distance: 203 - 204: 10.763 distance: 203 - 209: 29.976 distance: 204 - 236: 34.525 distance: 205 - 206: 8.921 distance: 206 - 207: 26.009 distance: 207 - 208: 32.429 distance: 209 - 210: 27.621 distance: 210 - 211: 35.214 distance: 210 - 213: 26.313 distance: 211 - 212: 24.636 distance: 211 - 217: 25.091 distance: 213 - 214: 22.172 distance: 214 - 215: 13.768 distance: 214 - 216: 13.139