Starting phenix.real_space_refine on Sun Jul 5 07:59:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fd3_29001/07_2026/8fd3_29001.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fd3_29001/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8fd3_29001/07_2026/8fd3_29001.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fd3_29001/07_2026/8fd3_29001.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fd3_29001/07_2026/8fd3_29001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fd3_29001/07_2026/8fd3_29001.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fd3_29001/07_2026/8fd3_29001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fd3_29001/07_2026/8fd3_29001.map" } 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-dev-6108/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: {'RNA': 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: 4.96, 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: 1.97 Conformation dependent library (CDL) restraints added in 969.0 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: 3.32 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: 5.34 Time building geometry restraints manager: 2.73 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: 36551 2.36 - 4.73: 350 4.73 - 7.09: 40 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=" 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 angle pdb=" N LEU A 198 " pdb=" CA LEU A 198 " pdb=" C LEU A 198 " ideal model delta sigma weight residual 111.40 106.13 5.27 1.22e+00 6.72e-01 1.86e+01 ... (remaining 36945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 15256 35.84 - 71.68: 649 71.68 - 107.52: 32 107.52 - 143.37: 1 143.37 - 179.21: 5 Dihedral angle restraints: 15943 sinusoidal: 7218 harmonic: 8725 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 44.62 155.38 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 73.27 126.73 1 1.50e+01 4.44e-03 6.82e+01 dihedral pdb=" O4' C M 50 " pdb=" C1' C M 50 " pdb=" N1 C M 50 " pdb=" C2 C M 50 " ideal model delta sinusoidal sigma weight residual -128.00 51.21 -179.21 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2823 0.036 - 0.073: 794 0.073 - 0.109: 268 0.109 - 0.146: 59 0.146 - 0.182: 13 Chirality restraints: 3957 Sorted by residual: chirality pdb=" CA PRO F 247 " pdb=" N PRO F 247 " pdb=" C PRO F 247 " pdb=" CB PRO F 247 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CA TYR I 334 " pdb=" N TYR I 334 " pdb=" C TYR I 334 " pdb=" CB TYR I 334 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" C1' U M 20 " pdb=" O4' U M 20 " pdb=" C2' U M 20 " pdb=" N1 U M 20 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.48e-01 ... (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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 25.300 Find NCS groups from input model: 0.380 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- 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= 0.167 Angle : 0.578 11.822 36950 Z= 0.328 Chirality : 0.040 0.182 3957 Planarity : 0.004 0.092 4421 Dihedral : 17.742 179.206 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 0.00291 / 0.17 (27069) covalent geometry : angle 0.57823 / 0.33 (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 : 0.747 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: 0.1712 time to fit residues: 135.0443 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 : 0.731 ------------------------------------------------------------------------------- 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 283 GLN H 30 ASN H 84 HIS 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 J 81 HIS ** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.141102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.105545 restraints weight = 57012.038| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.07 r_work: 0.3535 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.143 27069 Z= 0.394 Angle : 0.889 23.165 36950 Z= 0.457 Chirality : 0.052 0.332 3957 Planarity : 0.007 0.099 4421 Dihedral : 15.008 178.519 4335 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.54 % Favored : 94.09 % Rotamer: Outliers : 5.14 % Allowed : 18.00 % Favored : 76.86 % 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: -0.35 (0.15), residues: 2943 helix: 0.66 (0.15), residues: 1029 sheet: -0.98 (0.22), residues: 576 loop : -0.45 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 117 TYR 0.030 0.003 TYR H 219 PHE 0.034 0.003 PHE C 98 TRP 0.032 0.003 TRP A 176 HIS 0.011 0.002 HIS L 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.39 (27069) covalent geometry : angle 0.88866 / 0.46 (36950) hydrogen bonds : bond 0.05001 / 3.33 ( 1077) hydrogen bonds : angle 5.51604 / 3.90 ( 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 389 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 253 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 TYR cc_start: 0.7830 (m-80) cc_final: 0.7601 (m-80) REVERT: B 204 MET cc_start: 0.6553 (mtp) cc_final: 0.6254 (mtm) REVERT: C 42 GLN cc_start: 0.7490 (tt0) cc_final: 0.7093 (tt0) REVERT: D 134 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8045 (p0) REVERT: D 261 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8209 (mm-30) REVERT: E 64 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8359 (tt) REVERT: E 77 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8226 (ttp80) REVERT: E 83 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: E 261 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: F 42 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: F 251 GLU cc_start: 0.5320 (OUTLIER) cc_final: 0.4863 (pp20) REVERT: G 33 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7824 (mt) REVERT: G 74 LEU cc_start: 0.9114 (tp) cc_final: 0.8890 (tp) REVERT: G 137 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7150 (tmm) REVERT: G 224 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7962 (t0) REVERT: H 142 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7689 (mtt) REVERT: H 240 TYR cc_start: 0.7751 (m-80) cc_final: 0.7398 (m-80) REVERT: H 251 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7640 (mt-10) REVERT: I 44 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7645 (mpt180) REVERT: I 136 GLN cc_start: 0.8178 (mt0) cc_final: 0.7906 (mp10) REVERT: I 139 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6420 (t80) REVERT: I 256 GLN cc_start: 0.7629 (mt0) cc_final: 0.6874 (tp40) REVERT: I 303 MET cc_start: 0.8033 (mmm) cc_final: 0.7787 (mmm) REVERT: J 47 ARG cc_start: 0.8833 (ttm110) cc_final: 0.8166 (ttm110) REVERT: K 43 LYS cc_start: 0.7629 (pttm) cc_final: 0.7409 (mtpt) REVERT: K 95 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: L 78 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7245 (t80) outliers start: 136 outliers final: 49 residues processed: 372 average time/residue: 0.1738 time to fit residues: 101.0425 Evaluate side-chains 268 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 203 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 206 THR Chi-restraints excluded: chain B residue 23 ILE 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 78 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 64 LEU 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 57 SER Chi-restraints excluded: chain F residue 75 VAL 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 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 44 ARG Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 109 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 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 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: 4.9990 chunk 288 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** 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** G 42 GLN G 135 GLN G 218 ASN H 284 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.143191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.108239 restraints weight = 57282.494| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.35 r_work: 0.3572 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27069 Z= 0.147 Angle : 0.608 17.666 36950 Z= 0.319 Chirality : 0.042 0.209 3957 Planarity : 0.004 0.082 4421 Dihedral : 14.648 178.214 4303 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.93 % Favored : 94.77 % Rotamer: Outliers : 3.02 % Allowed : 18.68 % Favored : 78.30 % 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: 1029 sheet: -0.83 (0.22), residues: 565 loop : -0.46 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 69 TYR 0.024 0.001 TYR F 244 PHE 0.022 0.001 PHE A 137 TRP 0.029 0.001 TRP A 176 HIS 0.004 0.001 HIS F 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (27069) covalent geometry : angle 0.60846 / 0.32 (36950) hydrogen bonds : bond 0.03804 / 2.55 ( 1077) hydrogen bonds : angle 5.00625 / 3.52 ( 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 321 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 241 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7344 (tt0) cc_final: 0.6956 (pt0) REVERT: B 138 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6544 (mm-40) REVERT: B 141 ASN cc_start: 0.6345 (m110) cc_final: 0.6063 (t0) REVERT: C 261 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: D 142 MET cc_start: 0.8781 (ttp) cc_final: 0.8382 (ttp) REVERT: D 261 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: E 34 ARG cc_start: 0.6746 (mmm-85) cc_final: 0.6533 (mmm160) REVERT: E 77 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8143 (ttp80) REVERT: E 254 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8265 (mp) REVERT: E 261 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: F 42 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: G 74 LEU cc_start: 0.9089 (tp) cc_final: 0.8824 (tp) REVERT: H 14 TYR cc_start: 0.8102 (m-80) cc_final: 0.7405 (m-80) REVERT: H 87 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8341 (ttm-80) REVERT: H 142 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7574 (mtp) REVERT: H 248 LYS cc_start: 0.8268 (mptt) cc_final: 0.7905 (mptt) REVERT: I 136 GLN cc_start: 0.8199 (mt0) cc_final: 0.7916 (mp10) REVERT: I 139 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6574 (t80) REVERT: I 177 LEU cc_start: 0.6968 (mp) cc_final: 0.6583 (mm) REVERT: I 194 GLU cc_start: 0.6682 (mp0) cc_final: 0.6235 (mp0) REVERT: I 256 GLN cc_start: 0.7603 (mt0) cc_final: 0.6900 (tp40) REVERT: J 82 GLN cc_start: 0.4976 (OUTLIER) cc_final: 0.3901 (mt0) REVERT: J 95 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: K 43 LYS cc_start: 0.7521 (pttm) cc_final: 0.7250 (mtpt) outliers start: 80 outliers final: 34 residues processed: 307 average time/residue: 0.1671 time to fit residues: 81.7004 Evaluate side-chains 248 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 97 SER Chi-restraints excluded: chain A residue 206 THR 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 210 VAL Chi-restraints excluded: chain C residue 261 GLU 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 254 LEU 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 284 GLN 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 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 67 ASP Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain K residue 41 ILE 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: 10.0000 chunk 93 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 244 optimal weight: 30.0000 chunk 282 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** D 283 GLN E 30 ASN E 283 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN H 42 GLN H 284 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.139630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.103782 restraints weight = 56876.303| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.02 r_work: 0.3506 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27069 Z= 0.235 Angle : 0.642 18.336 36950 Z= 0.334 Chirality : 0.044 0.222 3957 Planarity : 0.005 0.084 4421 Dihedral : 14.614 179.389 4293 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.61 % Favored : 94.09 % Rotamer: Outliers : 3.25 % Allowed : 18.71 % Favored : 78.03 % 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: -0.13 (0.16), residues: 2943 helix: 1.01 (0.16), residues: 1034 sheet: -0.87 (0.23), residues: 540 loop : -0.51 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 47 TYR 0.026 0.002 TYR F 244 PHE 0.033 0.002 PHE I 53 TRP 0.040 0.002 TRP I 488 HIS 0.008 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.24 (27069) covalent geometry : angle 0.64161 / 0.33 (36950) hydrogen bonds : bond 0.03786 / 2.55 ( 1077) hydrogen bonds : angle 5.00395 / 3.51 ( 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 296 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 210 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7612 (tt0) cc_final: 0.7358 (tt0) REVERT: C 261 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: D 142 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8195 (ttp) REVERT: D 226 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7595 (mp) REVERT: D 261 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: E 34 ARG cc_start: 0.7012 (mmm-85) cc_final: 0.6784 (mmm160) REVERT: E 77 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8149 (ttp80) REVERT: E 137 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7483 (tmm) REVERT: E 152 ASP cc_start: 0.7292 (p0) cc_final: 0.6796 (p0) REVERT: E 254 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8371 (mp) REVERT: E 261 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: F 15 TYR cc_start: 0.8179 (m-80) cc_final: 0.7662 (m-80) REVERT: F 42 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: G 137 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7379 (tmm) REVERT: H 87 ARG cc_start: 0.8805 (ttm-80) cc_final: 0.8484 (ttm-80) REVERT: H 142 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7624 (mtt) REVERT: H 248 LYS cc_start: 0.8386 (mptt) cc_final: 0.8074 (mptt) REVERT: I 136 GLN cc_start: 0.8034 (mt0) cc_final: 0.7815 (mp10) REVERT: I 139 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6503 (t80) REVERT: I 256 GLN cc_start: 0.7678 (mt0) cc_final: 0.6916 (tp40) REVERT: J 8 ASP cc_start: 0.8462 (m-30) cc_final: 0.8042 (p0) REVERT: J 82 GLN cc_start: 0.5162 (OUTLIER) cc_final: 0.3917 (mt0) REVERT: K 43 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7296 (mtpt) REVERT: K 82 GLN cc_start: 0.7544 (tm-30) cc_final: 0.7342 (mt0) outliers start: 86 outliers final: 47 residues processed: 273 average time/residue: 0.1515 time to fit residues: 66.6731 Evaluate side-chains 257 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 97 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE 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 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 64 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 261 GLU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 149 THR 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 42 GLN Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 294 ASN 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 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 166 HIS Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 82 GLN 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 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: 0.5980 chunk 175 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 26 optimal weight: 30.0000 chunk 195 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** C 215 ASN ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN E 283 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN G 135 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** ** 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 = 0.4395 r_free = 0.4395 target = 0.140051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.105636 restraints weight = 56620.396| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.50 r_work: 0.3515 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27069 Z= 0.163 Angle : 0.589 16.617 36950 Z= 0.309 Chirality : 0.042 0.216 3957 Planarity : 0.004 0.086 4421 Dihedral : 14.537 179.572 4293 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.44 % Favored : 94.33 % Rotamer: Outliers : 3.59 % Allowed : 18.83 % Favored : 77.58 % 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: -0.04 (0.16), residues: 2943 helix: 1.10 (0.16), residues: 1033 sheet: -0.85 (0.23), residues: 540 loop : -0.46 (0.17), residues: 1370 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 0.044 0.001 PHE I 53 TRP 0.044 0.002 TRP A 176 HIS 0.004 0.001 HIS I 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (27069) covalent geometry : angle 0.58892 / 0.31 (36950) hydrogen bonds : bond 0.03461 / 2.33 ( 1077) hydrogen bonds : angle 4.85225 / 3.40 ( 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 310 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 215 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7640 (tt0) cc_final: 0.7366 (tt0) REVERT: B 138 GLN cc_start: 0.6893 (mm110) cc_final: 0.6549 (mm-40) REVERT: B 141 ASN cc_start: 0.6418 (m110) cc_final: 0.6081 (t0) REVERT: C 179 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6023 (mtp85) REVERT: C 261 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: D 226 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7585 (mp) REVERT: D 261 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7892 (mm-30) REVERT: E 34 ARG cc_start: 0.7003 (mmm-85) cc_final: 0.6780 (mmm160) REVERT: E 77 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8165 (ttp80) REVERT: E 152 ASP cc_start: 0.7380 (p0) cc_final: 0.6875 (p0) REVERT: E 181 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8312 (pt0) REVERT: E 254 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8338 (mp) REVERT: E 305 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8294 (ttt) REVERT: F 15 TYR cc_start: 0.8133 (m-80) cc_final: 0.7713 (m-80) REVERT: F 42 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: F 64 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7813 (mt) REVERT: G 137 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7428 (tmm) REVERT: H 87 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8494 (ttm-80) REVERT: H 142 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7575 (mtt) REVERT: H 248 LYS cc_start: 0.8334 (mptt) cc_final: 0.8084 (mptt) REVERT: I 139 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6360 (t80) REVERT: I 364 GLU cc_start: 0.3948 (OUTLIER) cc_final: 0.3625 (pm20) REVERT: J 82 GLN cc_start: 0.5215 (OUTLIER) cc_final: 0.3936 (mt0) REVERT: J 95 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: K 43 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7268 (mtpt) REVERT: K 82 GLN cc_start: 0.7569 (tm-30) cc_final: 0.7330 (mt0) outliers start: 95 outliers final: 52 residues processed: 285 average time/residue: 0.1553 time to fit residues: 72.2276 Evaluate side-chains 267 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 198 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 71 LEU Chi-restraints excluded: chain B residue 163 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 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 64 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 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 33 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 305 MET 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 284 GLN Chi-restraints excluded: chain F residue 311 THR 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 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 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 I residue 364 GLU Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 95 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 157 optimal weight: 0.0020 chunk 165 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 269 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- 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** ** 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 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** ** 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 = 0.4381 r_free = 0.4381 target = 0.139105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.103713 restraints weight = 56658.976| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.00 r_work: 0.3507 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27069 Z= 0.169 Angle : 0.586 16.470 36950 Z= 0.306 Chirality : 0.041 0.214 3957 Planarity : 0.004 0.088 4421 Dihedral : 14.498 179.970 4293 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.61 % Favored : 94.16 % Rotamer: Outliers : 3.52 % Allowed : 18.94 % Favored : 77.54 % 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: 1.14 (0.16), residues: 1030 sheet: -0.91 (0.22), residues: 569 loop : -0.46 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 47 TYR 0.026 0.001 TYR F 244 PHE 0.016 0.001 PHE L 61 TRP 0.045 0.002 TRP A 176 HIS 0.004 0.001 HIS J 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (27069) covalent geometry : angle 0.58642 / 0.31 (36950) hydrogen bonds : bond 0.03409 / 2.30 ( 1077) hydrogen bonds : angle 4.78832 / 3.36 ( 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 289 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 196 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 179 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6064 (mtp85) REVERT: C 261 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: D 226 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7626 (mp) REVERT: D 261 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: E 34 ARG cc_start: 0.6990 (mmm-85) cc_final: 0.6764 (mmm160) REVERT: E 77 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8188 (ttp80) REVERT: E 137 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7404 (tmm) REVERT: E 152 ASP cc_start: 0.7377 (p0) cc_final: 0.6890 (p0) REVERT: E 181 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8375 (pt0) REVERT: E 254 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8362 (mp) REVERT: E 305 MET cc_start: 0.8560 (ttt) cc_final: 0.8303 (ttt) REVERT: F 15 TYR cc_start: 0.8147 (m-80) cc_final: 0.7677 (m-80) REVERT: F 42 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: F 64 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7876 (mt) REVERT: G 137 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7481 (tmm) REVERT: H 87 ARG cc_start: 0.8831 (ttm-80) cc_final: 0.8500 (ttm-80) REVERT: H 179 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7603 (mtp85) REVERT: H 248 LYS cc_start: 0.8385 (mptt) cc_final: 0.8061 (mptt) REVERT: I 139 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6391 (t80) REVERT: I 295 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7412 (tttp) REVERT: I 298 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.5134 (mmm160) REVERT: I 364 GLU cc_start: 0.4011 (OUTLIER) cc_final: 0.3665 (pm20) REVERT: J 82 GLN cc_start: 0.5305 (OUTLIER) cc_final: 0.3953 (mt0) REVERT: J 95 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: K 43 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7278 (mtpt) outliers start: 93 outliers final: 56 residues processed: 268 average time/residue: 0.1578 time to fit residues: 67.9574 Evaluate side-chains 264 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 189 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 71 LEU 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 64 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 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 33 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 77 ARG 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 254 LEU 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 G residue 57 SER 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 210 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE 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 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 298 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 95 GLN 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 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: 0.9990 chunk 52 optimal weight: 9.9990 chunk 273 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 GLN H 256 GLN H 284 GLN I 101 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** 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 = 0.4388 r_free = 0.4388 target = 0.139588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104315 restraints weight = 56394.911| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.93 r_work: 0.3527 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5223 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= 0.134 Angle : 0.567 15.539 36950 Z= 0.296 Chirality : 0.041 0.207 3957 Planarity : 0.004 0.089 4421 Dihedral : 14.492 179.304 4293 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.47 % Favored : 94.29 % Rotamer: Outliers : 3.02 % Allowed : 19.66 % Favored : 77.32 % 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: 0.00 (0.16), residues: 2943 helix: 1.17 (0.16), residues: 1032 sheet: -0.81 (0.22), residues: 564 loop : -0.45 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 47 TYR 0.025 0.001 TYR F 244 PHE 0.014 0.001 PHE L 61 TRP 0.040 0.001 TRP A 176 HIS 0.008 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (27069) covalent geometry : angle 0.56743 / 0.30 (36950) hydrogen bonds : bond 0.03278 / 2.21 ( 1077) hydrogen bonds : angle 4.70128 / 3.30 ( 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 276 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 196 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8204 (t-170) cc_final: 0.7966 (t-170) REVERT: B 43 HIS cc_start: 0.7395 (t70) cc_final: 0.7073 (t-90) REVERT: C 179 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.5997 (mtp85) REVERT: C 221 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: C 261 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: D 226 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7599 (mp) REVERT: D 261 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: E 34 ARG cc_start: 0.7013 (mmm-85) cc_final: 0.6796 (mmm160) REVERT: E 77 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8197 (ttp80) REVERT: E 137 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7463 (tmm) REVERT: E 152 ASP cc_start: 0.7226 (p0) cc_final: 0.6735 (p0) REVERT: E 181 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: E 254 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8334 (mp) REVERT: E 305 MET cc_start: 0.8575 (ttt) cc_final: 0.8319 (ttt) REVERT: F 15 TYR cc_start: 0.8113 (m-80) cc_final: 0.7701 (m-80) REVERT: F 42 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: F 64 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7804 (mt) REVERT: H 248 LYS cc_start: 0.8387 (mptt) cc_final: 0.8112 (mptt) REVERT: I 139 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.6338 (t80) REVERT: I 364 GLU cc_start: 0.3994 (OUTLIER) cc_final: 0.3657 (pm20) REVERT: J 82 GLN cc_start: 0.5336 (OUTLIER) cc_final: 0.3942 (mt0) REVERT: K 43 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7274 (mtpt) outliers start: 80 outliers final: 54 residues processed: 258 average time/residue: 0.1507 time to fit residues: 63.2446 Evaluate side-chains 255 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 186 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 63 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 LEU 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 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 64 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 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 77 ARG 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 E residue 254 LEU 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 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 210 VAL 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 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 364 GLU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 82 GLN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 35 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 253 optimal weight: 20.0000 chunk 238 optimal weight: 0.0980 chunk 289 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 278 optimal weight: 0.0770 overall best weight: 2.8344 ------------------------------------------------------------------------------- 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** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN E 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN H 256 GLN H 284 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN K 82 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.138240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.102841 restraints weight = 57148.718| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 3.18 r_work: 0.3479 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27069 Z= 0.196 Angle : 0.591 16.376 36950 Z= 0.308 Chirality : 0.042 0.214 3957 Planarity : 0.005 0.090 4421 Dihedral : 14.470 178.977 4293 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.67 % Favored : 94.09 % Rotamer: Outliers : 3.67 % Allowed : 19.09 % Favored : 77.24 % 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: 0.01 (0.16), residues: 2943 helix: 1.17 (0.16), residues: 1032 sheet: -0.84 (0.22), residues: 566 loop : -0.42 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 47 TYR 0.025 0.002 TYR F 244 PHE 0.017 0.001 PHE K 61 TRP 0.037 0.001 TRP A 176 HIS 0.007 0.001 HIS K 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (27069) covalent geometry : angle 0.59060 / 0.31 (36950) hydrogen bonds : bond 0.03418 / 2.30 ( 1077) hydrogen bonds : angle 4.72816 / 3.31 ( 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 288 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 191 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8224 (t-170) cc_final: 0.7987 (t-170) REVERT: B 43 HIS cc_start: 0.7400 (t70) cc_final: 0.7075 (t-90) REVERT: C 179 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6039 (mtp85) REVERT: C 221 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: C 261 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: D 142 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8131 (ttp) REVERT: D 226 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7605 (mp) REVERT: E 34 ARG cc_start: 0.7110 (mmm-85) cc_final: 0.6852 (mmm160) REVERT: E 77 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8125 (ttp80) REVERT: E 137 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7451 (tmm) REVERT: E 152 ASP cc_start: 0.7376 (p0) cc_final: 0.6879 (p0) REVERT: E 181 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8357 (pt0) REVERT: E 254 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8409 (mp) REVERT: E 305 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8322 (ttt) REVERT: F 42 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: F 64 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7944 (mt) REVERT: G 137 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7533 (tmm) REVERT: H 87 ARG cc_start: 0.8852 (ttm-80) cc_final: 0.8513 (ttm-80) REVERT: H 113 GLU cc_start: 0.8022 (pp20) cc_final: 0.7740 (pp20) REVERT: H 179 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7612 (mtp85) REVERT: H 248 LYS cc_start: 0.8447 (mptt) cc_final: 0.8159 (mptt) REVERT: I 139 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.6391 (t80) REVERT: I 295 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7441 (tttp) REVERT: I 298 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.5405 (mmm160) REVERT: I 364 GLU cc_start: 0.4104 (OUTLIER) cc_final: 0.3729 (pm20) REVERT: J 95 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: K 43 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7311 (mtpt) outliers start: 97 outliers final: 61 residues processed: 265 average time/residue: 0.1590 time to fit residues: 67.7542 Evaluate side-chains 266 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 185 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 23 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 163 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 64 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 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 77 ARG 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 254 LEU Chi-restraints excluded: chain E residue 305 MET 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 311 THR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 137 MET 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 210 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE 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 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 298 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 95 GLN 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 Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 72 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 214 optimal weight: 30.0000 chunk 102 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 271 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS ** B 77 HIS ** 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 E 30 ASN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN H 284 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.138481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.103202 restraints weight = 56685.572| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.01 r_work: 0.3497 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5593 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= 0.155 Angle : 0.582 16.052 36950 Z= 0.302 Chirality : 0.041 0.208 3957 Planarity : 0.005 0.090 4421 Dihedral : 14.456 179.220 4293 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.71 % Favored : 94.05 % Rotamer: Outliers : 2.99 % Allowed : 19.92 % Favored : 77.09 % 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: 0.08 (0.16), residues: 2943 helix: 1.24 (0.16), residues: 1026 sheet: -0.82 (0.22), residues: 556 loop : -0.39 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 47 TYR 0.024 0.001 TYR F 244 PHE 0.015 0.001 PHE L 61 TRP 0.062 0.001 TRP I 488 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (27069) covalent geometry : angle 0.58188 / 0.30 (36950) hydrogen bonds : bond 0.03317 / 2.24 ( 1077) hydrogen bonds : angle 4.70146 / 3.29 ( 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 269 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 190 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8296 (t-170) cc_final: 0.8046 (t-170) REVERT: B 43 HIS cc_start: 0.7368 (t70) cc_final: 0.7058 (t-90) REVERT: C 179 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.6061 (mtp85) REVERT: C 205 MET cc_start: 0.8214 (mmm) cc_final: 0.7754 (mmm) REVERT: C 221 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: C 261 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: D 142 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8113 (ttp) REVERT: D 226 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7592 (mp) REVERT: E 77 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8121 (ttp80) REVERT: E 137 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7432 (tmm) REVERT: E 152 ASP cc_start: 0.7340 (p0) cc_final: 0.6848 (p0) REVERT: E 181 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8330 (pt0) REVERT: E 305 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8306 (ttt) REVERT: F 42 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: F 64 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7879 (mt) REVERT: H 87 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.8528 (ttm-80) REVERT: H 113 GLU cc_start: 0.7989 (pp20) cc_final: 0.7702 (pp20) REVERT: H 179 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7317 (mtp85) REVERT: H 248 LYS cc_start: 0.8428 (mptt) cc_final: 0.8091 (mptt) REVERT: I 139 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.6447 (t80) REVERT: I 295 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7466 (tttp) REVERT: I 298 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5517 (mmm160) REVERT: I 364 GLU cc_start: 0.4106 (OUTLIER) cc_final: 0.3731 (pm20) REVERT: J 20 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: J 95 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7413 (mp10) REVERT: K 43 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7274 (mtpt) REVERT: K 71 ARG cc_start: 0.8681 (mtp85) cc_final: 0.8030 (mtm-85) outliers start: 79 outliers final: 56 residues processed: 252 average time/residue: 0.1596 time to fit residues: 64.9642 Evaluate side-chains 258 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 183 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 195 MET 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 163 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 64 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 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 77 ARG 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 305 MET 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 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 H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE 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 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 298 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 95 GLN 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 53 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 294 optimal weight: 50.0000 chunk 200 optimal weight: 4.9990 chunk 261 optimal weight: 0.0770 chunk 7 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 151 optimal weight: 0.0670 overall best weight: 1.8080 ------------------------------------------------------------------------------- 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** ** 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** G 42 GLN H 284 GLN ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 ASN ** K 82 GLN ** 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 = 0.4372 r_free = 0.4372 target = 0.138488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.103224 restraints weight = 56535.720| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.10 r_work: 0.3489 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 27069 Z= 0.190 Angle : 0.731 59.200 36950 Z= 0.402 Chirality : 0.043 0.621 3957 Planarity : 0.005 0.116 4421 Dihedral : 14.458 179.209 4293 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.61 % Favored : 94.16 % Rotamer: Outliers : 3.36 % Allowed : 19.66 % Favored : 76.98 % Cbeta Deviations : 0.07 % 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: 0.08 (0.16), residues: 2943 helix: 1.24 (0.16), residues: 1026 sheet: -0.82 (0.22), residues: 556 loop : -0.39 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG J 47 TYR 0.042 0.001 TYR I 399 PHE 0.015 0.001 PHE L 61 TRP 0.107 0.002 TRP I 488 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (27069) covalent geometry : angle 0.73070 / 0.40 (36950) hydrogen bonds : bond 0.03313 / 2.24 ( 1077) hydrogen bonds : angle 4.70189 / 3.29 ( 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 272 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 183 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8298 (t-170) cc_final: 0.8049 (t-170) REVERT: B 43 HIS cc_start: 0.7379 (t70) cc_final: 0.7064 (t-90) REVERT: C 179 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6052 (mtp85) REVERT: C 205 MET cc_start: 0.8231 (mmm) cc_final: 0.7759 (mmm) REVERT: C 221 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: C 261 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: D 142 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8124 (ttp) REVERT: D 226 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7603 (mp) REVERT: E 77 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8121 (ttp80) REVERT: E 137 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7396 (tmm) REVERT: E 152 ASP cc_start: 0.7358 (p0) cc_final: 0.6836 (p0) REVERT: E 181 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: E 305 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8325 (ttt) REVERT: F 42 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: F 64 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7880 (mt) REVERT: H 87 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8525 (ttm-80) REVERT: H 113 GLU cc_start: 0.7997 (pp20) cc_final: 0.7727 (pp20) REVERT: H 144 MET cc_start: 0.8629 (mtm) cc_final: 0.8403 (mtm) REVERT: H 179 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7312 (mtp85) REVERT: H 248 LYS cc_start: 0.8429 (mptt) cc_final: 0.8091 (mptt) REVERT: I 139 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.6448 (t80) REVERT: I 295 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7464 (tttp) REVERT: I 298 ARG cc_start: 0.5998 (OUTLIER) cc_final: 0.5519 (mmm160) REVERT: I 364 GLU cc_start: 0.4112 (OUTLIER) cc_final: 0.3731 (pm20) REVERT: J 20 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: J 95 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7420 (mp10) REVERT: K 43 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7273 (mtpt) REVERT: K 71 ARG cc_start: 0.8688 (mtp85) cc_final: 0.8036 (mtm-85) outliers start: 89 outliers final: 66 residues processed: 247 average time/residue: 0.1660 time to fit residues: 65.8565 Evaluate side-chains 267 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 182 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 195 MET 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 139 MET Chi-restraints excluded: chain B residue 163 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 29 LEU 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 64 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 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 77 ARG 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 305 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 40 ILE 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 311 THR Chi-restraints excluded: chain G residue 57 SER 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 H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE 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 237 TYR Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 69 ILE 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 298 ARG Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 364 GLU Chi-restraints excluded: chain J residue 7 GLU Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 77 TYR Chi-restraints excluded: chain J residue 95 GLN Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 13 ILE 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 8 ASP 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: 3.9990 chunk 214 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** ** 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** G 42 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 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 = 0.4372 r_free = 0.4372 target = 0.138486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.103088 restraints weight = 56262.452| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.10 r_work: 0.3491 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 27069 Z= 0.190 Angle : 0.731 59.200 36950 Z= 0.402 Chirality : 0.043 0.621 3957 Planarity : 0.005 0.116 4421 Dihedral : 14.458 179.209 4293 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.61 % Favored : 94.16 % Rotamer: Outliers : 3.21 % Allowed : 19.77 % Favored : 77.01 % Cbeta Deviations : 0.07 % 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: 0.08 (0.16), residues: 2943 helix: 1.24 (0.16), residues: 1026 sheet: -0.82 (0.22), residues: 556 loop : -0.39 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG J 47 TYR 0.042 0.001 TYR I 399 PHE 0.015 0.001 PHE L 61 TRP 0.107 0.002 TRP I 488 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 (27069) covalent geometry : angle 0.73070 / 0.40 (36950) hydrogen bonds : bond 0.03313 / 2.24 ( 1077) hydrogen bonds : angle 4.70189 / 3.29 ( 3165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6234.22 seconds wall clock time: 120 minutes 37.48 seconds (7237.48 seconds total)