Starting phenix.real_space_refine on Sat Aug 8 07:03:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fd3_29001/08_2026/8fd3_29001.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fd3_29001/08_2026/8fd3_29001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fd3_29001/08_2026/8fd3_29001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fd3_29001/08_2026/8fd3_29001.map" model { file = "/net/cci-nas-00/data/ceres_data/8fd3_29001/08_2026/8fd3_29001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fd3_29001/08_2026/8fd3_29001.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fd3_29001/08_2026/8fd3_29001.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fd3_29001/08_2026/8fd3_29001.cif" } resolution = 3.12 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= 0.013 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 408 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 85 5.49 5 S 94 5.16 5 C 16536 2.51 5 N 4460 2.21 5 O 5075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26250 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1727 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2345 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2351 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "H" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2420 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNAv2': 63} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 10, 'rna3p_pur': 18, 'rna3p_pyr': 20} Link IDs: {'rna2p': 25, 'rna3p': 37} Chain: "N" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "O" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 4.94, per 1000 atoms: 0.19 Number of scatterers: 26250 At special positions: 0 Unit cell: (101.184, 115.94, 198.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 85 15.00 O 5075 8.00 N 4460 7.00 C 16536 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: 2.19 Conformation dependent library (CDL) restraints added in 846.8 milliseconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5590 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 51 sheets defined 39.4% alpha, 23.4% beta 12 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.584A pdb=" N TRP A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 40 through 45 removed outlier: 4.325A pdb=" N GLU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.817A pdb=" N MET B 204 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.618A pdb=" N THR B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.729A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 196 through 206 removed outlier: 3.572A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.645A pdb=" N SER C 214 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.552A pdb=" N GLY C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.661A pdb=" N ASP C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.576A pdb=" N ILE D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.522A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.784A pdb=" N GLY D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.084A pdb=" N ASP D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.598A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.521A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.883A pdb=" N GLY E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 277 through 284 removed outlier: 4.092A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 301 through 318 Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.643A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.772A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.826A pdb=" N GLY F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.957A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 56 through 71 removed outlier: 3.748A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 206 removed outlier: 3.644A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 277 through 284 removed outlier: 4.009A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 318 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 56 through 71 removed outlier: 3.531A pdb=" N ILE H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 109 through 112 Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 206 removed outlier: 3.573A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.679A pdb=" N GLY H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 270 No H-bonds generated for 'chain 'H' and resid 268 through 270' Processing helix chain 'H' and resid 277 through 285 removed outlier: 3.921A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.604A pdb=" N LYS H 295 " --> pdb=" O PRO H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 317 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.747A pdb=" N ILE I 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.585A pdb=" N ALA I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 116 through 118 No H-bonds generated for 'chain 'I' and resid 116 through 118' Processing helix chain 'I' and resid 148 through 157 removed outlier: 5.400A pdb=" N ALA I 153 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 removed outlier: 3.505A pdb=" N GLN I 187 " --> pdb=" O ALA I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 251 through 252 No H-bonds generated for 'chain 'I' and resid 251 through 252' Processing helix chain 'I' and resid 253 through 256 Processing helix chain 'I' and resid 261 through 270 removed outlier: 3.502A pdb=" N ALA I 265 " --> pdb=" O SER I 261 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR I 270 " --> pdb=" O GLY I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 Processing helix chain 'I' and resid 361 through 367 removed outlier: 3.668A pdb=" N LYS I 365 " --> pdb=" O ASN I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 382 removed outlier: 4.030A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU I 379 " --> pdb=" O LEU I 375 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE I 380 " --> pdb=" O PHE I 376 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER I 381 " --> pdb=" O ASN I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 392 Processing helix chain 'I' and resid 397 through 421 removed outlier: 3.686A pdb=" N ILE I 417 " --> pdb=" O ASN I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 removed outlier: 3.834A pdb=" N LYS I 432 " --> pdb=" O PRO I 428 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS I 443 " --> pdb=" O GLU I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 460 Processing helix chain 'I' and resid 463 through 469 Processing helix chain 'I' and resid 469 through 480 Processing helix chain 'I' and resid 481 through 495 Processing helix chain 'J' and resid 6 through 33 Processing helix chain 'J' and resid 41 through 53 Processing helix chain 'J' and resid 58 through 72 removed outlier: 5.964A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 removed outlier: 3.716A pdb=" N ILE J 85 " --> pdb=" O HIS J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 107 Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.526A pdb=" N LYS J 111 " --> pdb=" O TYR J 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 removed outlier: 3.817A pdb=" N VAL K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 73 removed outlier: 3.604A pdb=" N GLY K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 93 through 107 Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.768A pdb=" N CYS L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.805A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 Processing helix chain 'L' and resid 81 through 92 Processing helix chain 'L' and resid 93 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.913A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.522A pdb=" N LEU A 57 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N ARG A 165 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 6.588A pdb=" N PHE A 13 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER A 97 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.025A pdb=" N ARG B 19 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 100 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.358A pdb=" N LEU B 109 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N GLU B 10 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N LYS B 107 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 9.120A pdb=" N VAL B 12 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N ASP B 105 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 removed outlier: 5.582A pdb=" N VAL B 179 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG B 118 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 181 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR B 116 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.659A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.659A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR C 180 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 15 " --> pdb=" O TRP C 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP C 230 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR C 17 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE C 228 " --> pdb=" O TYR C 17 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 19 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 226 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 21 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.661A pdb=" N GLY C 25 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 155 through 160 removed outlier: 3.545A pdb=" N SER C 169 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR D 180 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.541A pdb=" N GLY D 25 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.996A pdb=" N THR D 39 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AC2, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 244 Processing sheet with id=AC4, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'E' and resid 106 through 107 Processing sheet with id=AC9, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AD1, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.531A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD6, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.520A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.520A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY G 276 " --> pdb=" O TYR G 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AE1, first strand: chain 'G' and resid 77 through 80 removed outlier: 3.633A pdb=" N ILE G 85 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 106 through 107 removed outlier: 3.673A pdb=" N PHE G 106 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AE4, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR H 15 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP H 230 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE7, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AE8, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE9, first strand: chain 'H' and resid 105 through 107 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.569A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AF3, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.476A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AF5, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.255A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 329 through 333 1110 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 6.65 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7329 1.33 - 1.45: 5312 1.45 - 1.57: 14112 1.57 - 1.69: 167 1.69 - 1.81: 149 Bond restraints: 27069 Sorted by residual: bond pdb=" C1' DA O 12 " pdb=" N9 DA O 12 " ideal model delta sigma weight residual 1.468 1.403 0.065 1.40e-02 5.10e+03 2.16e+01 bond pdb=" C3' DG O 10 " pdb=" C2' DG O 10 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 5.96e+00 bond pdb=" C1' DT O 9 " pdb=" N1 DT O 9 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.71e+00 bond pdb=" CA SER F 28 " pdb=" C SER F 28 " ideal model delta sigma weight residual 1.532 1.502 0.030 1.41e-02 5.03e+03 4.62e+00 bond pdb=" C1' DT N 61 " pdb=" N1 DT N 61 " ideal model delta sigma weight residual 1.468 1.497 -0.029 1.40e-02 5.10e+03 4.35e+00 ... (remaining 27064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 36350 2.36 - 4.73: 527 4.73 - 7.09: 64 7.09 - 9.46: 7 9.46 - 11.82: 2 Bond angle restraints: 36950 Sorted by residual: angle pdb=" N SER E 28 " pdb=" CA SER E 28 " pdb=" C SER E 28 " ideal model delta sigma weight residual 110.44 103.41 7.03 1.20e+00 6.94e-01 3.43e+01 angle pdb=" N LEU E 29 " pdb=" CA LEU E 29 " pdb=" C LEU E 29 " ideal model delta sigma weight residual 111.03 117.42 -6.39 1.11e+00 8.12e-01 3.31e+01 angle pdb=" N TYR H 244 " pdb=" CA TYR H 244 " pdb=" C TYR H 244 " ideal model delta sigma weight residual 114.56 108.27 6.29 1.27e+00 6.20e-01 2.45e+01 angle pdb=" C3' G M 48 " pdb=" O3' G M 48 " pdb=" P U M 49 " ideal model delta sigma weight residual 119.70 125.57 -5.87 1.20e+00 6.94e-01 2.39e+01 angle pdb=" C ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta sigma weight residual 117.23 111.04 6.19 1.36e+00 5.41e-01 2.07e+01 ... (remaining 36945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.28: 15017 33.28 - 66.55: 861 66.55 - 99.83: 63 99.83 - 133.11: 1 133.11 - 166.39: 1 Dihedral angle restraints: 15943 sinusoidal: 7218 harmonic: 8725 Sorted by residual: dihedral pdb=" C4' U M 52 " pdb=" C3' U M 52 " pdb=" C2' U M 52 " pdb=" C1' U M 52 " ideal model delta sinusoidal sigma weight residual 36.34 -36.64 72.99 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' G M 33 " pdb=" C3' G M 33 " pdb=" C2' G M 33 " pdb=" C1' G M 33 " ideal model delta sinusoidal sigma weight residual 36.34 -36.53 72.88 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' U M 45 " pdb=" C3' U M 45 " pdb=" C2' U M 45 " pdb=" C1' U M 45 " ideal model delta sinusoidal sigma weight residual 36.34 -36.21 72.56 1 3.10e+00 1.04e-01 7.00e+02 ... (remaining 15940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3472 0.068 - 0.136: 359 0.136 - 0.204: 25 0.204 - 0.273: 77 0.273 - 0.341: 24 Chirality restraints: 3957 Sorted by residual: chirality pdb=" P U M 49 " pdb=" OP1 U M 49 " pdb=" OP2 U M 49 " pdb=" O5' U M 49 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" P G M 48 " pdb=" OP1 G M 48 " pdb=" OP2 G M 48 " pdb=" O5' G M 48 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" P C M 4 " pdb=" OP1 C M 4 " pdb=" OP2 C M 4 " pdb=" O5' C M 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 3954 not shown) Planarity restraints: 4421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " 0.060 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO F 247 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C PHE J 61 " -0.064 2.00e-02 2.50e+03 pdb=" O PHE J 61 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS J 62 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 209 " 0.042 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO B 210 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " 0.036 5.00e-02 4.00e+02 ... (remaining 4418 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 823 2.69 - 3.24: 25236 3.24 - 3.79: 43362 3.79 - 4.35: 59913 4.35 - 4.90: 96751 Nonbonded interactions: 226085 Sorted by model distance: nonbonded pdb=" O LEU B 184 " pdb=" ND2 ASN B 185 " model vdw 2.137 3.120 nonbonded pdb=" N GLU G 257 " pdb=" OE1 GLU G 257 " model vdw 2.194 3.120 nonbonded pdb=" OG1 THR A 15 " pdb=" NE2 GLN A 143 " model vdw 2.202 3.120 nonbonded pdb=" N GLU J 83 " pdb=" OE1 GLU J 83 " model vdw 2.206 3.120 nonbonded pdb=" OG1 THR E 19 " pdb=" O SER E 239 " model vdw 2.220 3.040 ... (remaining 226080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = (chain 'G' and (resid 12 through 109 or resid 133 through 319)) selection = (chain 'H' and (resid 12 through 109 or resid 133 through 319)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 26.730 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27069 Z= 0.170 Angle : 0.641 11.822 36950 Z= 0.343 Chirality : 0.057 0.341 3957 Planarity : 0.004 0.092 4421 Dihedral : 18.496 166.386 10353 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.40 % Favored : 94.29 % Rotamer: Outliers : 2.76 % Allowed : 20.76 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 are not related in a simple way. whole: 0.44 (0.16), residues: 2943 helix: 1.67 (0.17), residues: 1013 sheet: -0.65 (0.22), residues: 596 loop : -0.22 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 96 TYR 0.020 0.001 TYR I 334 PHE 0.016 0.001 PHE J 26 TRP 0.015 0.001 TRP I 488 HIS 0.004 0.001 HIS I 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (27069) covalent geometry : angle 0.64097 / 0.34 (36950) hydrogen bonds : bond 0.16765 / 11.17 ( 1077) hydrogen bonds : angle 6.71669 / 4.66 ( 3165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 457 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.5729 (tmm) cc_final: 0.5497 (tmm) REVERT: B 204 MET cc_start: 0.6695 (mtp) cc_final: 0.6236 (ptt) REVERT: C 42 GLN cc_start: 0.6925 (tt0) cc_final: 0.6538 (tt0) REVERT: C 71 GLN cc_start: 0.8218 (tp40) cc_final: 0.7780 (mm110) REVERT: C 84 HIS cc_start: 0.6689 (m90) cc_final: 0.5936 (t70) REVERT: D 134 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7793 (p0) REVERT: D 142 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7684 (ttp) REVERT: E 108 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6776 (tt) REVERT: E 305 MET cc_start: 0.7683 (ttp) cc_final: 0.7458 (ttt) REVERT: F 15 TYR cc_start: 0.7257 (m-80) cc_final: 0.6846 (m-80) REVERT: F 29 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6564 (mt) REVERT: F 187 ASP cc_start: 0.7583 (t0) cc_final: 0.7359 (t70) REVERT: G 78 VAL cc_start: 0.8948 (t) cc_final: 0.8717 (m) REVERT: G 137 MET cc_start: 0.7318 (tmm) cc_final: 0.6682 (tmm) REVERT: H 45 TYR cc_start: 0.6114 (m-80) cc_final: 0.5886 (m-80) REVERT: I 157 CYS cc_start: 0.3626 (m) cc_final: 0.2823 (m) REVERT: I 347 LEU cc_start: 0.3980 (OUTLIER) cc_final: 0.3671 (mt) REVERT: I 382 ASN cc_start: 0.3665 (m-40) cc_final: 0.3123 (m-40) REVERT: J 52 LEU cc_start: 0.8653 (mt) cc_final: 0.8417 (mm) REVERT: L 102 LEU cc_start: 0.7780 (mt) cc_final: 0.7550 (mt) outliers start: 73 outliers final: 20 residues processed: 515 average time/residue: 0.1911 time to fit residues: 151.3422 Evaluate side-chains 259 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain J residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN C 47 ASN C 86 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN E 42 GLN E 229 GLN E 283 GLN F 30 ASN F 31 HIS F 76 ASN F 171 HIS F 181 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 283 GLN H 30 ASN H 134 ASN H 256 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.142286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.106716 restraints weight = 57666.466| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.46 r_work: 0.3543 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 27069 Z= 0.407 Angle : 1.187 22.646 36950 Z= 0.531 Chirality : 0.092 2.142 3957 Planarity : 0.007 0.082 4421 Dihedral : 14.767 160.167 4335 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.47 % Favored : 94.16 % Rotamer: Outliers : 5.22 % Allowed : 17.81 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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 are not related in a simple way. whole: -0.23 (0.16), residues: 2943 helix: 0.79 (0.16), residues: 1029 sheet: -0.92 (0.22), residues: 585 loop : -0.41 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 117 TYR 0.032 0.003 TYR I 40 PHE 0.025 0.003 PHE K 61 TRP 0.030 0.003 TRP A 176 HIS 0.008 0.002 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00920 / 0.41 (27069) covalent geometry : angle 1.18750 / 0.53 (36950) hydrogen bonds : bond 0.05120 / 3.42 ( 1077) hydrogen bonds : angle 5.49423 / 3.86 ( 3165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 243 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 TYR cc_start: 0.7824 (m-80) cc_final: 0.7607 (m-80) REVERT: C 227 VAL cc_start: 0.8422 (t) cc_final: 0.8123 (m) REVERT: C 261 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: D 134 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8111 (p0) REVERT: D 261 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8190 (mm-30) REVERT: E 77 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8017 (mtp180) REVERT: E 83 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: E 261 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: F 15 TYR cc_start: 0.8508 (m-80) cc_final: 0.8308 (m-80) REVERT: F 42 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: F 251 GLU cc_start: 0.5212 (OUTLIER) cc_final: 0.4729 (pp20) REVERT: G 33 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7984 (mp) REVERT: G 74 LEU cc_start: 0.9107 (tp) cc_final: 0.8868 (tp) REVERT: G 137 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7104 (tmm) REVERT: G 224 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7919 (t0) REVERT: H 85 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7734 (tp) REVERT: H 142 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7681 (mtt) REVERT: H 240 TYR cc_start: 0.7758 (m-80) cc_final: 0.7389 (m-80) REVERT: H 251 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7682 (mt-10) REVERT: I 20 ILE cc_start: 0.4898 (OUTLIER) cc_final: 0.4383 (tp) REVERT: I 136 GLN cc_start: 0.8158 (mt0) cc_final: 0.7883 (mp10) REVERT: I 139 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6527 (t80) REVERT: I 256 GLN cc_start: 0.7638 (mt0) cc_final: 0.6871 (tp40) REVERT: I 303 MET cc_start: 0.7905 (mmm) cc_final: 0.7602 (mmm) REVERT: J 47 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8130 (ttm110) REVERT: J 82 GLN cc_start: 0.4823 (OUTLIER) cc_final: 0.3978 (mt0) REVERT: K 43 LYS cc_start: 0.7637 (pttm) cc_final: 0.7396 (mtpt) REVERT: K 95 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: L 78 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7040 (t80) outliers start: 138 outliers final: 50 residues processed: 366 average time/residue: 0.1877 time to fit residues: 107.9406 Evaluate side-chains 271 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 435 ARG Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 95 GLN Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 78 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 203 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 288 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 283 GLN F 30 ASN F 181 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN G 42 GLN G 135 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.144842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.109371 restraints weight = 57784.471| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.29 r_work: 0.3630 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27069 Z= 0.153 Angle : 0.780 17.417 36950 Z= 0.366 Chirality : 0.069 1.463 3957 Planarity : 0.005 0.081 4421 Dihedral : 14.736 156.428 4313 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.16 % Favored : 94.53 % Rotamer: Outliers : 3.21 % Allowed : 18.41 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 are not related in a simple way. whole: -0.03 (0.16), residues: 2943 helix: 1.13 (0.16), residues: 1030 sheet: -0.81 (0.22), residues: 564 loop : -0.46 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 69 TYR 0.026 0.001 TYR F 244 PHE 0.026 0.001 PHE A 137 TRP 0.029 0.001 TRP I 488 HIS 0.004 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (27069) covalent geometry : angle 0.78010 / 0.37 (36950) hydrogen bonds : bond 0.03769 / 2.52 ( 1077) hydrogen bonds : angle 4.99999 / 3.50 ( 3165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 243 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7400 (tt0) cc_final: 0.6978 (pt0) REVERT: A 176 TRP cc_start: 0.5663 (t60) cc_final: 0.5457 (t60) REVERT: B 123 LYS cc_start: 0.5494 (OUTLIER) cc_final: 0.4857 (mtpp) REVERT: B 204 MET cc_start: 0.6164 (mtm) cc_final: 0.5877 (mtt) REVERT: C 261 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7850 (mm-30) REVERT: D 142 MET cc_start: 0.8706 (ttp) cc_final: 0.8289 (ttp) REVERT: D 261 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8079 (mm-30) REVERT: E 77 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7991 (ttp80) REVERT: E 137 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7334 (tmm) REVERT: E 261 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: F 42 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: F 251 GLU cc_start: 0.5090 (OUTLIER) cc_final: 0.4836 (pp20) REVERT: G 74 LEU cc_start: 0.9056 (tp) cc_final: 0.8808 (tp) REVERT: H 14 TYR cc_start: 0.7995 (m-80) cc_final: 0.7396 (m-80) REVERT: H 142 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7298 (mtp) REVERT: H 248 LYS cc_start: 0.8292 (mptt) cc_final: 0.7966 (mptt) REVERT: I 136 GLN cc_start: 0.8123 (mt0) cc_final: 0.7839 (mp10) REVERT: I 139 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6400 (t80) REVERT: I 177 LEU cc_start: 0.6965 (mp) cc_final: 0.6586 (mm) REVERT: I 256 GLN cc_start: 0.7570 (mt0) cc_final: 0.6866 (tp40) REVERT: I 405 VAL cc_start: 0.6468 (t) cc_final: 0.6195 (p) REVERT: J 95 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7211 (mp10) REVERT: K 7 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: K 43 LYS cc_start: 0.7499 (pttm) cc_final: 0.7244 (mtpt) outliers start: 85 outliers final: 36 residues processed: 308 average time/residue: 0.1734 time to fit residues: 86.0322 Evaluate side-chains 255 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 214 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 172 optimal weight: 0.1980 chunk 139 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 244 optimal weight: 30.0000 chunk 282 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN E 256 GLN E 283 GLN F 181 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN G 42 GLN G 135 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.138497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103442 restraints weight = 57016.808| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.50 r_work: 0.3479 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 27069 Z= 0.299 Angle : 0.855 19.986 36950 Z= 0.407 Chirality : 0.066 1.187 3957 Planarity : 0.005 0.085 4421 Dihedral : 14.761 169.122 4295 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.74 % Favored : 93.95 % Rotamer: Outliers : 3.52 % Allowed : 18.90 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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 are not related in a simple way. whole: -0.29 (0.15), residues: 2943 helix: 0.80 (0.16), residues: 1034 sheet: -0.89 (0.22), residues: 570 loop : -0.55 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 47 TYR 0.042 0.002 TYR I 399 PHE 0.035 0.002 PHE I 53 TRP 0.043 0.002 TRP I 488 HIS 0.007 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.30 (27069) covalent geometry : angle 0.85470 / 0.41 (36950) hydrogen bonds : bond 0.04158 / 2.82 ( 1077) hydrogen bonds : angle 5.14142 / 3.61 ( 3165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 208 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7666 (tt0) cc_final: 0.7384 (tt0) REVERT: A 176 TRP cc_start: 0.5953 (t-100) cc_final: 0.5660 (t60) REVERT: B 27 ASN cc_start: 0.7516 (p0) cc_final: 0.7314 (p0) REVERT: C 261 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: D 34 ARG cc_start: 0.6248 (mtt180) cc_final: 0.5990 (mtt180) REVERT: D 261 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: E 137 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7242 (tmm) REVERT: E 254 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8392 (mp) REVERT: E 261 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: E 305 MET cc_start: 0.8568 (ttt) cc_final: 0.8294 (ttt) REVERT: F 38 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8268 (mttp) REVERT: F 42 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: F 251 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.5213 (pp20) REVERT: H 40 ILE cc_start: 0.8723 (mm) cc_final: 0.8481 (mm) REVERT: H 142 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7739 (mtt) REVERT: H 244 TYR cc_start: 0.7198 (t80) cc_final: 0.6412 (t80) REVERT: H 248 LYS cc_start: 0.8472 (mptt) cc_final: 0.8145 (mptt) REVERT: I 139 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6593 (t80) REVERT: I 298 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.4865 (mmm160) REVERT: I 303 MET cc_start: 0.8397 (mmm) cc_final: 0.8068 (mmm) REVERT: I 331 ILE cc_start: 0.5046 (OUTLIER) cc_final: 0.4631 (mp) REVERT: K 43 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7318 (mtpt) REVERT: K 82 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7315 (mt0) outliers start: 93 outliers final: 54 residues processed: 280 average time/residue: 0.1687 time to fit residues: 77.3872 Evaluate side-chains 261 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 284 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 LYS Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 172 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 265 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN E 86 ASN F 181 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN G 42 GLN H 30 ASN H 42 GLN H 256 GLN H 284 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 382 ASN J 20 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.140683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.105745 restraints weight = 56784.605| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.04 r_work: 0.3552 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27069 Z= 0.146 Angle : 0.720 16.580 36950 Z= 0.338 Chirality : 0.060 1.131 3957 Planarity : 0.004 0.087 4421 Dihedral : 14.583 171.404 4293 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.54 % Favored : 94.26 % Rotamer: Outliers : 3.18 % Allowed : 19.92 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 are not related in a simple way. whole: -0.06 (0.16), residues: 2943 helix: 1.06 (0.16), residues: 1034 sheet: -0.90 (0.23), residues: 544 loop : -0.42 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 47 TYR 0.022 0.001 TYR F 244 PHE 0.039 0.001 PHE I 53 TRP 0.018 0.001 TRP I 488 HIS 0.003 0.001 HIS I 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (27069) covalent geometry : angle 0.71991 / 0.34 (36950) hydrogen bonds : bond 0.03416 / 2.30 ( 1077) hydrogen bonds : angle 4.82305 / 3.38 ( 3165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 217 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7678 (tt0) cc_final: 0.7381 (tt0) REVERT: A 176 TRP cc_start: 0.6015 (t-100) cc_final: 0.5658 (t60) REVERT: B 90 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7634 (mm110) REVERT: B 141 ASN cc_start: 0.6373 (m110) cc_final: 0.6158 (t0) REVERT: B 204 MET cc_start: 0.6816 (mtp) cc_final: 0.6578 (mtm) REVERT: C 261 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: D 226 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7547 (mp) REVERT: D 261 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: E 137 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7238 (tmm) REVERT: E 152 ASP cc_start: 0.7345 (p0) cc_final: 0.6891 (p0) REVERT: E 181 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8331 (pt0) REVERT: F 42 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: F 64 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7765 (mt) REVERT: H 142 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7467 (mtp) REVERT: H 248 LYS cc_start: 0.8364 (mptt) cc_final: 0.8073 (mptt) REVERT: I 139 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6451 (t80) REVERT: I 364 GLU cc_start: 0.3769 (OUTLIER) cc_final: 0.3463 (pm20) REVERT: J 20 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: K 43 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7213 (mtpt) outliers start: 84 outliers final: 40 residues processed: 285 average time/residue: 0.1689 time to fit residues: 78.7504 Evaluate side-chains 253 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 294 ASN Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 157 optimal weight: 0.0570 chunk 165 optimal weight: 6.9990 chunk 211 optimal weight: 20.0000 chunk 246 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 284 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.138709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.103820 restraints weight = 57004.243| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.36 r_work: 0.3502 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27069 Z= 0.212 Angle : 0.743 17.267 36950 Z= 0.350 Chirality : 0.059 1.108 3957 Planarity : 0.005 0.089 4421 Dihedral : 14.520 173.525 4293 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.78 % Favored : 94.02 % Rotamer: Outliers : 3.10 % Allowed : 19.77 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 are not related in a simple way. whole: -0.14 (0.16), residues: 2943 helix: 1.00 (0.16), residues: 1032 sheet: -0.92 (0.22), residues: 557 loop : -0.47 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 47 TYR 0.027 0.002 TYR I 399 PHE 0.040 0.002 PHE I 53 TRP 0.045 0.002 TRP I 488 HIS 0.004 0.001 HIS J 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (27069) covalent geometry : angle 0.74341 / 0.35 (36950) hydrogen bonds : bond 0.03569 / 2.43 ( 1077) hydrogen bonds : angle 4.84372 / 3.40 ( 3165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 202 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8231 (t-170) cc_final: 0.7955 (t-170) REVERT: A 176 TRP cc_start: 0.6155 (t-100) cc_final: 0.5701 (t60) REVERT: C 179 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.6071 (mtp85) REVERT: C 205 MET cc_start: 0.8211 (mmm) cc_final: 0.7910 (mmm) REVERT: C 261 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: D 142 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8133 (ttp) REVERT: D 226 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7636 (mp) REVERT: D 261 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: E 137 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7163 (tmm) REVERT: E 152 ASP cc_start: 0.7334 (p0) cc_final: 0.6879 (p0) REVERT: E 181 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: F 42 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: F 64 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7898 (mt) REVERT: H 40 ILE cc_start: 0.8698 (mm) cc_final: 0.8449 (mm) REVERT: H 179 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7849 (mtp85) REVERT: H 248 LYS cc_start: 0.8425 (mptt) cc_final: 0.8108 (mptt) REVERT: I 139 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6375 (t80) REVERT: I 295 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7444 (tttp) REVERT: I 364 GLU cc_start: 0.3998 (OUTLIER) cc_final: 0.3654 (pm20) REVERT: J 20 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: K 43 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7267 (mtpt) outliers start: 82 outliers final: 49 residues processed: 265 average time/residue: 0.1763 time to fit residues: 75.5076 Evaluate side-chains 255 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 191 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 115 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 GLN H 284 GLN I 101 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.140289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.105304 restraints weight = 56958.344| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.27 r_work: 0.3546 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27069 Z= 0.132 Angle : 0.699 15.675 36950 Z= 0.329 Chirality : 0.057 1.071 3957 Planarity : 0.004 0.090 4421 Dihedral : 14.462 175.160 4293 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.57 % Favored : 94.22 % Rotamer: Outliers : 2.76 % Allowed : 20.23 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 are not related in a simple way. whole: -0.03 (0.16), residues: 2943 helix: 1.12 (0.16), residues: 1032 sheet: -0.87 (0.22), residues: 571 loop : -0.42 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 47 TYR 0.022 0.001 TYR F 244 PHE 0.036 0.001 PHE I 53 TRP 0.028 0.001 TRP I 488 HIS 0.004 0.001 HIS K 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (27069) covalent geometry : angle 0.69937 / 0.33 (36950) hydrogen bonds : bond 0.03246 / 2.20 ( 1077) hydrogen bonds : angle 4.70182 / 3.29 ( 3165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 196 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8255 (t-170) cc_final: 0.7984 (t-170) REVERT: A 176 TRP cc_start: 0.6151 (t-100) cc_final: 0.5626 (t60) REVERT: B 43 HIS cc_start: 0.7278 (t70) cc_final: 0.6956 (t-90) REVERT: C 179 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6005 (mtp85) REVERT: C 221 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: C 261 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: D 142 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8195 (ttp) REVERT: D 226 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7590 (mp) REVERT: D 261 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: E 137 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7252 (tmm) REVERT: E 152 ASP cc_start: 0.7283 (p0) cc_final: 0.6810 (p0) REVERT: E 181 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8364 (pt0) REVERT: F 42 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: G 179 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7703 (mtp85) REVERT: H 248 LYS cc_start: 0.8387 (mptt) cc_final: 0.8100 (mptt) REVERT: I 139 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.6399 (t80) REVERT: I 364 GLU cc_start: 0.3769 (OUTLIER) cc_final: 0.3488 (pm20) REVERT: K 43 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7233 (mtpt) outliers start: 73 outliers final: 49 residues processed: 250 average time/residue: 0.1696 time to fit residues: 68.8644 Evaluate side-chains 250 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 237 TYR Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 35 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 238 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 GLN H 284 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.138911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.104316 restraints weight = 57119.896| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.47 r_work: 0.3514 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27069 Z= 0.171 Angle : 0.704 16.011 36950 Z= 0.332 Chirality : 0.056 1.043 3957 Planarity : 0.004 0.091 4421 Dihedral : 14.416 176.283 4293 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.37 % Favored : 94.43 % Rotamer: Outliers : 2.95 % Allowed : 20.15 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 are not related in a simple way. whole: 0.05 (0.16), residues: 2943 helix: 1.18 (0.16), residues: 1026 sheet: -0.83 (0.22), residues: 571 loop : -0.36 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 47 TYR 0.023 0.001 TYR F 244 PHE 0.036 0.001 PHE I 53 TRP 0.065 0.001 TRP I 488 HIS 0.008 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (27069) covalent geometry : angle 0.70420 / 0.33 (36950) hydrogen bonds : bond 0.03325 / 2.26 ( 1077) hydrogen bonds : angle 4.70162 / 3.29 ( 3165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 197 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8304 (t-170) cc_final: 0.8044 (t-170) REVERT: A 176 TRP cc_start: 0.6208 (t-100) cc_final: 0.5641 (t60) REVERT: B 43 HIS cc_start: 0.7414 (t70) cc_final: 0.7072 (t-90) REVERT: C 179 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6041 (mtp85) REVERT: C 221 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: C 261 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: D 142 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8200 (ttp) REVERT: D 226 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7581 (mp) REVERT: D 261 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: E 137 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7123 (tmm) REVERT: E 152 ASP cc_start: 0.7409 (p0) cc_final: 0.6920 (p0) REVERT: E 181 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8391 (pt0) REVERT: F 42 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: F 64 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7869 (mt) REVERT: H 113 GLU cc_start: 0.8000 (pp20) cc_final: 0.7739 (pp20) REVERT: H 248 LYS cc_start: 0.8446 (mptt) cc_final: 0.8149 (mptt) REVERT: I 139 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6371 (t80) REVERT: I 364 GLU cc_start: 0.3758 (OUTLIER) cc_final: 0.3514 (pm20) REVERT: I 399 TYR cc_start: 0.6043 (OUTLIER) cc_final: 0.5302 (t80) REVERT: K 43 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7257 (mtpt) REVERT: K 71 ARG cc_start: 0.8648 (mtp85) cc_final: 0.7975 (mtm-85) outliers start: 78 outliers final: 51 residues processed: 256 average time/residue: 0.1647 time to fit residues: 68.4400 Evaluate side-chains 254 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 72 optimal weight: 3.9990 chunk 223 optimal weight: 30.0000 chunk 214 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 ASN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.136853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.102392 restraints weight = 57349.924| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.21 r_work: 0.3460 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 27069 Z= 0.253 Angle : 0.759 18.164 36950 Z= 0.362 Chirality : 0.058 1.008 3957 Planarity : 0.005 0.092 4421 Dihedral : 14.469 177.440 4293 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.18 % Favored : 93.61 % Rotamer: Outliers : 3.21 % Allowed : 19.85 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 are not related in a simple way. whole: -0.07 (0.16), residues: 2943 helix: 1.05 (0.16), residues: 1026 sheet: -0.91 (0.23), residues: 548 loop : -0.42 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 47 TYR 0.021 0.002 TYR F 244 PHE 0.032 0.002 PHE I 53 TRP 0.056 0.002 TRP I 488 HIS 0.024 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (27069) covalent geometry : angle 0.75874 / 0.36 (36950) hydrogen bonds : bond 0.03687 / 2.52 ( 1077) hydrogen bonds : angle 4.83333 / 3.39 ( 3165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 189 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8394 (t-170) cc_final: 0.8101 (t-90) REVERT: A 176 TRP cc_start: 0.6399 (t-100) cc_final: 0.5768 (t60) REVERT: B 43 HIS cc_start: 0.7443 (t70) cc_final: 0.7094 (t-90) REVERT: B 77 HIS cc_start: 0.7615 (p90) cc_final: 0.6946 (p-80) REVERT: C 179 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6071 (mtp85) REVERT: C 221 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: C 261 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: D 226 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7562 (mp) REVERT: E 137 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7134 (tmm) REVERT: E 152 ASP cc_start: 0.7548 (p0) cc_final: 0.7095 (p0) REVERT: E 181 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8582 (pt0) REVERT: F 42 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: F 64 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7964 (mt) REVERT: H 40 ILE cc_start: 0.8903 (mm) cc_final: 0.8686 (mm) REVERT: H 113 GLU cc_start: 0.8001 (pp20) cc_final: 0.7763 (pp20) REVERT: H 179 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7428 (mtp85) REVERT: H 248 LYS cc_start: 0.8510 (mptt) cc_final: 0.8105 (mptt) REVERT: I 139 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.6458 (t80) REVERT: I 295 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7504 (tttp) REVERT: I 364 GLU cc_start: 0.3959 (OUTLIER) cc_final: 0.3682 (pm20) REVERT: I 399 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.5472 (t80) REVERT: K 43 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7292 (mtpt) outliers start: 85 outliers final: 58 residues processed: 258 average time/residue: 0.1584 time to fit residues: 66.3841 Evaluate side-chains 255 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 183 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 ARG Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 287 ASN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 53 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 294 optimal weight: 40.0000 chunk 200 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 GLN H 284 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.136826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.101427 restraints weight = 56749.276| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.95 r_work: 0.3462 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27069 Z= 0.206 Angle : 0.729 16.898 36950 Z= 0.347 Chirality : 0.056 0.977 3957 Planarity : 0.005 0.093 4421 Dihedral : 14.409 178.303 4293 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.88 % Favored : 93.92 % Rotamer: Outliers : 2.72 % Allowed : 20.38 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 are not related in a simple way. whole: -0.09 (0.16), residues: 2943 helix: 1.04 (0.16), residues: 1027 sheet: -0.89 (0.22), residues: 558 loop : -0.44 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 47 TYR 0.023 0.002 TYR F 244 PHE 0.031 0.002 PHE I 53 TRP 0.056 0.002 TRP I 488 HIS 0.004 0.001 HIS I 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (27069) covalent geometry : angle 0.72931 / 0.35 (36950) hydrogen bonds : bond 0.03517 / 2.40 ( 1077) hydrogen bonds : angle 4.78608 / 3.36 ( 3165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 188 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8313 (t-170) cc_final: 0.7999 (t-90) REVERT: A 176 TRP cc_start: 0.6414 (t-100) cc_final: 0.5765 (t60) REVERT: B 43 HIS cc_start: 0.7384 (t70) cc_final: 0.7158 (t-90) REVERT: B 77 HIS cc_start: 0.7599 (p90) cc_final: 0.6872 (p-80) REVERT: C 179 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6080 (mtp85) REVERT: C 221 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: C 227 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8668 (m) REVERT: C 261 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: D 226 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7583 (mp) REVERT: E 137 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7111 (tmm) REVERT: E 152 ASP cc_start: 0.7536 (p0) cc_final: 0.7107 (p0) REVERT: E 181 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: F 42 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: F 64 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7945 (mt) REVERT: H 40 ILE cc_start: 0.8910 (mm) cc_final: 0.8688 (mm) REVERT: H 113 GLU cc_start: 0.7963 (pp20) cc_final: 0.7701 (pp20) REVERT: H 248 LYS cc_start: 0.8496 (mptt) cc_final: 0.8144 (mptt) REVERT: I 139 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.6480 (t80) REVERT: I 295 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7528 (tttp) REVERT: I 364 GLU cc_start: 0.3953 (OUTLIER) cc_final: 0.3676 (pm20) REVERT: I 399 TYR cc_start: 0.6695 (OUTLIER) cc_final: 0.5462 (t80) REVERT: K 43 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7319 (mtpt) REVERT: K 71 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8114 (mtm-85) outliers start: 72 outliers final: 54 residues processed: 247 average time/residue: 0.1689 time to fit residues: 67.4936 Evaluate side-chains 251 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 336 GLN Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 399 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 112 optimal weight: 0.7980 chunk 214 optimal weight: 30.0000 chunk 35 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 249 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.136883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101496 restraints weight = 56441.168| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.95 r_work: 0.3462 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.278 27069 Z= 0.240 Angle : 0.838 59.196 36950 Z= 0.435 Chirality : 0.058 0.977 3957 Planarity : 0.005 0.093 4421 Dihedral : 14.407 178.301 4293 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.95 % Favored : 93.85 % Rotamer: Outliers : 2.76 % Allowed : 20.45 % Favored : 76.79 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.91 % 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 are not related in a simple way. whole: -0.09 (0.16), residues: 2943 helix: 1.04 (0.16), residues: 1027 sheet: -0.89 (0.22), residues: 558 loop : -0.44 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 47 TYR 0.021 0.002 TYR F 244 PHE 0.031 0.001 PHE I 53 TRP 0.049 0.002 TRP I 488 HIS 0.003 0.001 HIS I 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 (27069) covalent geometry : angle 0.83833 / 0.44 (36950) hydrogen bonds : bond 0.03511 / 2.39 ( 1077) hydrogen bonds : angle 4.78587 / 3.36 ( 3165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7173.74 seconds wall clock time: 123 minutes 38.90 seconds (7418.90 seconds total)