Starting phenix.real_space_refine on Fri Mar 6 01:46:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5n_26356/03_2026/7u5n_26356.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5n_26356/03_2026/7u5n_26356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u5n_26356/03_2026/7u5n_26356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5n_26356/03_2026/7u5n_26356.map" model { file = "/net/cci-nas-00/data/ceres_data/7u5n_26356/03_2026/7u5n_26356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5n_26356/03_2026/7u5n_26356.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 10 7.51 5 S 220 5.16 5 C 17240 2.51 5 N 4760 2.21 5 O 5050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27280 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 2.45, per 1000 atoms: 0.09 Number of scatterers: 27280 At special positions: 0 Unit cell: (135.89, 131.61, 108.07, 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) Mn 10 24.99 S 220 16.00 O 5050 8.00 N 4760 7.00 C 17240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.2 seconds 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6220 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 20 sheets defined 37.6% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 10 through 19 removed outlier: 3.760A pdb=" N LYS B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE B 68 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 233 removed outlier: 4.222A pdb=" N GLY B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.689A pdb=" N ASP B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE C 68 " --> pdb=" O SER C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 266 through 280 removed outlier: 3.740A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 280 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP C 289 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 333 Processing helix chain 'C' and resid 347 through 360 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS D 14 " --> pdb=" O ASN D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.963A pdb=" N PHE D 68 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 289 removed outlier: 3.689A pdb=" N ASP D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 347 through 360 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 10 through 19 removed outlier: 3.760A pdb=" N LYS E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE E 68 " --> pdb=" O SER E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 280 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP E 289 " --> pdb=" O ILE E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 333 Processing helix chain 'E' and resid 347 through 360 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS F 14 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 65 through 68 removed outlier: 3.965A pdb=" N PHE F 68 " --> pdb=" O SER F 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 65 through 68' Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY F 215 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 266 through 280 removed outlier: 3.740A pdb=" N LYS F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP F 289 " --> pdb=" O ILE F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 333 Processing helix chain 'F' and resid 347 through 360 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS G 14 " --> pdb=" O ASN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE G 68 " --> pdb=" O SER G 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 65 through 68' Processing helix chain 'G' and resid 113 through 124 Processing helix chain 'G' and resid 172 through 187 removed outlier: 3.665A pdb=" N VAL G 176 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 Processing helix chain 'G' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG G 280 " --> pdb=" O LYS G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP G 289 " --> pdb=" O ILE G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'H' and resid 4 through 9 Processing helix chain 'H' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS H 14 " --> pdb=" O ASN H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE H 68 " --> pdb=" O SER H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 113 through 124 Processing helix chain 'H' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL H 176 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 266 through 280 removed outlier: 3.740A pdb=" N LYS H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG H 280 " --> pdb=" O LYS H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 289 removed outlier: 3.689A pdb=" N ASP H 289 " --> pdb=" O ILE H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 333 Processing helix chain 'H' and resid 347 through 360 Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 10 through 19 removed outlier: 3.760A pdb=" N LYS I 14 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE I 68 " --> pdb=" O SER I 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 65 through 68' Processing helix chain 'I' and resid 113 through 124 Processing helix chain 'I' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL I 176 " --> pdb=" O GLY I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 233 removed outlier: 4.222A pdb=" N GLY I 215 " --> pdb=" O GLY I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 263 Processing helix chain 'I' and resid 266 through 280 removed outlier: 3.740A pdb=" N LYS I 279 " --> pdb=" O GLU I 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG I 280 " --> pdb=" O LYS I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 289 removed outlier: 3.691A pdb=" N ASP I 289 " --> pdb=" O ILE I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 333 Processing helix chain 'I' and resid 347 through 360 Processing helix chain 'J' and resid 4 through 9 Processing helix chain 'J' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS J 14 " --> pdb=" O ASN J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'J' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE J 68 " --> pdb=" O SER J 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 65 through 68' Processing helix chain 'J' and resid 113 through 124 Processing helix chain 'J' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL J 176 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 233 removed outlier: 4.222A pdb=" N GLY J 215 " --> pdb=" O GLY J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 263 Processing helix chain 'J' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS J 279 " --> pdb=" O GLU J 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG J 280 " --> pdb=" O LYS J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP J 289 " --> pdb=" O ILE J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 333 Processing helix chain 'J' and resid 347 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE A 98 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 96 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE A 33 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 101 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS A 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA B 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE B 190 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY B 207 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 192 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE A 98 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 96 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE A 33 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 101 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS A 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA B 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE B 190 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY B 207 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 192 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237 Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.240A pdb=" N PHE A 131 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 192 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY A 207 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE A 190 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY A 191 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA A 195 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS E 42 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE E 33 " --> pdb=" O CYS E 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL E 101 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU E 96 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET E 84 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE E 98 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.739A pdb=" N PHE B 98 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 96 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 33 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 101 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS B 42 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA C 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C 190 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C 207 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY C 192 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE C 131 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.739A pdb=" N PHE B 98 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 96 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 33 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 101 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS B 42 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA C 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C 190 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C 207 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY C 192 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE C 131 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE C 98 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 96 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE C 33 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 101 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS C 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA D 195 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY D 191 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE D 190 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY D 207 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 192 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE C 98 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 96 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE C 33 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 101 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS C 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA D 195 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY D 191 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE D 190 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY D 207 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 192 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.737A pdb=" N PHE D 98 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET D 84 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 96 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE D 33 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 101 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N CYS D 42 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA E 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY E 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE E 190 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY E 207 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY E 192 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE E 131 " --> pdb=" O PRO E 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.737A pdb=" N PHE D 98 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET D 84 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 96 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE D 33 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 101 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N CYS D 42 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA E 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY E 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE E 190 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY E 207 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY E 192 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE E 131 " --> pdb=" O PRO E 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE F 98 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET F 84 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU F 96 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE F 33 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL F 101 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS F 42 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA G 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY G 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE G 190 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY G 207 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY G 192 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE G 131 " --> pdb=" O PRO G 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE F 98 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET F 84 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU F 96 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE F 33 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL F 101 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS F 42 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA G 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY G 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE G 190 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY G 207 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY G 192 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE G 131 " --> pdb=" O PRO G 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 235 through 237 Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 237 removed outlier: 6.240A pdb=" N PHE F 131 " --> pdb=" O PRO F 208 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY F 192 " --> pdb=" O GLN F 205 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY F 207 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE F 190 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY F 191 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA F 195 " --> pdb=" O CYS J 42 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS J 42 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE J 33 " --> pdb=" O CYS J 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL J 101 " --> pdb=" O ILE J 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU J 96 " --> pdb=" O MET J 84 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET J 84 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE J 98 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.737A pdb=" N PHE G 98 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET G 84 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU G 96 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE G 33 " --> pdb=" O CYS G 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL G 101 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS G 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA H 195 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY H 191 " --> pdb=" O THR G 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE H 190 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY H 207 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY H 192 " --> pdb=" O GLN H 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE H 131 " --> pdb=" O PRO H 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.737A pdb=" N PHE G 98 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET G 84 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU G 96 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE G 33 " --> pdb=" O CYS G 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL G 101 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS G 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA H 195 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY H 191 " --> pdb=" O THR G 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE H 190 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY H 207 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY H 192 " --> pdb=" O GLN H 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE H 131 " --> pdb=" O PRO H 208 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE H 98 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET H 84 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU H 96 " --> pdb=" O MET H 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE H 33 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL H 101 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS H 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA I 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY I 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE I 190 " --> pdb=" O GLY I 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY I 207 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY I 192 " --> pdb=" O GLN I 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE H 98 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET H 84 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU H 96 " --> pdb=" O MET H 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE H 33 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL H 101 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS H 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA I 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY I 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE I 190 " --> pdb=" O GLY I 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY I 207 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY I 192 " --> pdb=" O GLN I 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE I 98 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET I 84 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU I 96 " --> pdb=" O MET I 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE I 33 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL I 101 " --> pdb=" O ILE I 33 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS I 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA J 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY J 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE J 190 " --> pdb=" O GLY J 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY J 207 " --> pdb=" O ILE J 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY J 192 " --> pdb=" O GLN J 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE J 131 " --> pdb=" O PRO J 208 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE I 98 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET I 84 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU I 96 " --> pdb=" O MET I 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE I 33 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL I 101 " --> pdb=" O ILE I 33 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS I 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA J 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY J 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE J 190 " --> pdb=" O GLY J 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY J 207 " --> pdb=" O ILE J 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY J 192 " --> pdb=" O GLN J 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE J 131 " --> pdb=" O PRO J 208 " (cutoff:3.500A) 1550 hydrogen bonds defined for protein. 4212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7322 1.33 - 1.45: 5427 1.45 - 1.57: 14951 1.57 - 1.69: 0 1.69 - 1.81: 330 Bond restraints: 28030 Sorted by residual: bond pdb=" C TRP G 149 " pdb=" N PRO G 150 " ideal model delta sigma weight residual 1.331 1.374 -0.044 1.31e-02 5.83e+03 1.12e+01 bond pdb=" C TRP A 149 " pdb=" N PRO A 150 " ideal model delta sigma weight residual 1.331 1.374 -0.044 1.31e-02 5.83e+03 1.11e+01 bond pdb=" C TRP H 149 " pdb=" N PRO H 150 " ideal model delta sigma weight residual 1.331 1.374 -0.044 1.31e-02 5.83e+03 1.11e+01 bond pdb=" C TRP E 149 " pdb=" N PRO E 150 " ideal model delta sigma weight residual 1.331 1.374 -0.043 1.31e-02 5.83e+03 1.10e+01 bond pdb=" C TRP J 149 " pdb=" N PRO J 150 " ideal model delta sigma weight residual 1.331 1.374 -0.043 1.31e-02 5.83e+03 1.10e+01 ... (remaining 28025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 36257 2.04 - 4.08: 1373 4.08 - 6.12: 140 6.12 - 8.15: 90 8.15 - 10.19: 30 Bond angle restraints: 37890 Sorted by residual: angle pdb=" N LYS G 95 " pdb=" CA LYS G 95 " pdb=" C LYS G 95 " ideal model delta sigma weight residual 109.40 119.59 -10.19 1.63e+00 3.76e-01 3.91e+01 angle pdb=" N LYS E 95 " pdb=" CA LYS E 95 " pdb=" C LYS E 95 " ideal model delta sigma weight residual 109.40 119.57 -10.17 1.63e+00 3.76e-01 3.89e+01 angle pdb=" N LYS J 95 " pdb=" CA LYS J 95 " pdb=" C LYS J 95 " ideal model delta sigma weight residual 109.40 119.57 -10.17 1.63e+00 3.76e-01 3.89e+01 angle pdb=" N LYS H 95 " pdb=" CA LYS H 95 " pdb=" C LYS H 95 " ideal model delta sigma weight residual 109.40 119.56 -10.16 1.63e+00 3.76e-01 3.89e+01 angle pdb=" N LYS B 95 " pdb=" CA LYS B 95 " pdb=" C LYS B 95 " ideal model delta sigma weight residual 109.40 119.55 -10.15 1.63e+00 3.76e-01 3.88e+01 ... (remaining 37885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 15172 15.43 - 30.85: 1095 30.85 - 46.28: 303 46.28 - 61.70: 70 61.70 - 77.13: 40 Dihedral angle restraints: 16680 sinusoidal: 6900 harmonic: 9780 Sorted by residual: dihedral pdb=" CA PRO G 160 " pdb=" C PRO G 160 " pdb=" N TYR G 161 " pdb=" CA TYR G 161 " ideal model delta harmonic sigma weight residual -180.00 -163.97 -16.03 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA PRO F 160 " pdb=" C PRO F 160 " pdb=" N TYR F 161 " pdb=" CA TYR F 161 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA PRO A 160 " pdb=" C PRO A 160 " pdb=" N TYR A 161 " pdb=" CA TYR A 161 " ideal model delta harmonic sigma weight residual -180.00 -164.00 -16.00 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 16677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2743 0.053 - 0.105: 735 0.105 - 0.158: 185 0.158 - 0.210: 56 0.210 - 0.263: 61 Chirality restraints: 3780 Sorted by residual: chirality pdb=" CA LYS I 91 " pdb=" N LYS I 91 " pdb=" C LYS I 91 " pdb=" CB LYS I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA LYS D 91 " pdb=" N LYS D 91 " pdb=" C LYS D 91 " pdb=" CB LYS D 91 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA LYS B 91 " pdb=" N LYS B 91 " pdb=" C LYS B 91 " pdb=" CB LYS B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3777 not shown) Planarity restraints: 5030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 159 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO H 160 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 160 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 160 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 159 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO E 160 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 160 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 160 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 159 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO I 160 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO I 160 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 160 " 0.027 5.00e-02 4.00e+02 ... (remaining 5027 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6998 2.79 - 3.32: 24718 3.32 - 3.84: 48036 3.84 - 4.37: 58879 4.37 - 4.90: 97312 Nonbonded interactions: 235943 Sorted by model distance: nonbonded pdb=" OH TYR A 180 " pdb=" OG1 THR E 46 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR I 46 " pdb=" OH TYR J 180 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR D 46 " pdb=" OH TYR E 180 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR F 180 " pdb=" OG1 THR J 46 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR H 46 " pdb=" OH TYR I 180 " model vdw 2.266 3.040 ... (remaining 235938 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 28030 Z= 0.326 Angle : 0.920 10.193 37890 Z= 0.569 Chirality : 0.061 0.263 3780 Planarity : 0.005 0.048 5030 Dihedral : 12.590 77.128 10460 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.44 % Allowed : 7.07 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.60 (0.14), residues: 3390 helix: 1.36 (0.15), residues: 1090 sheet: -0.51 (0.17), residues: 840 loop : 0.43 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 45 TYR 0.009 0.001 TYR C 137 PHE 0.020 0.002 PHE E 337 TRP 0.008 0.002 TRP E 32 HIS 0.004 0.001 HIS E 284 Details of bonding type rmsd covalent geometry : bond 0.00552 (28030) covalent geometry : angle 0.92047 (37890) hydrogen bonds : bond 0.16576 ( 1270) hydrogen bonds : angle 7.44548 ( 4212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 615 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8041 (tttp) cc_final: 0.7803 (tttm) REVERT: A 120 ILE cc_start: 0.8728 (mm) cc_final: 0.8521 (mm) REVERT: A 173 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8583 (ttm-80) REVERT: A 334 LYS cc_start: 0.7261 (pttt) cc_final: 0.7054 (pttt) REVERT: B 76 ASP cc_start: 0.7908 (p0) cc_final: 0.7678 (p0) REVERT: B 77 MET cc_start: 0.9040 (mmm) cc_final: 0.8824 (mtp) REVERT: B 106 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7670 (mpt180) REVERT: B 107 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7687 (mmtm) REVERT: B 119 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7778 (mtp85) REVERT: B 173 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8320 (ttm110) REVERT: B 210 GLU cc_start: 0.7732 (tp30) cc_final: 0.7153 (tp30) REVERT: B 336 TYR cc_start: 0.7762 (p90) cc_final: 0.7032 (p90) REVERT: B 363 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7473 (mt-10) REVERT: C 18 MET cc_start: 0.8984 (mmm) cc_final: 0.8775 (mmm) REVERT: C 84 MET cc_start: 0.8944 (ttp) cc_final: 0.8714 (ttp) REVERT: C 119 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7746 (mtp85) REVERT: C 263 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7173 (mt-10) REVERT: C 271 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7642 (mm-30) REVERT: C 334 LYS cc_start: 0.7415 (pttt) cc_final: 0.6852 (ptpp) REVERT: C 340 ARG cc_start: 0.7365 (ttm170) cc_final: 0.7155 (ttm110) REVERT: D 17 TYR cc_start: 0.9196 (m-80) cc_final: 0.8914 (m-80) REVERT: D 69 GLN cc_start: 0.8869 (pt0) cc_final: 0.8606 (pt0) REVERT: D 76 ASP cc_start: 0.8063 (p0) cc_final: 0.7850 (p0) REVERT: D 198 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8338 (mmp) REVERT: D 334 LYS cc_start: 0.7271 (pttt) cc_final: 0.6937 (ptpp) REVERT: E 24 ASP cc_start: 0.7944 (p0) cc_final: 0.7727 (p0) REVERT: E 69 GLN cc_start: 0.8935 (pt0) cc_final: 0.8708 (pt0) REVERT: E 119 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7768 (mtp85) REVERT: E 122 ASP cc_start: 0.8251 (m-30) cc_final: 0.8044 (m-30) REVERT: E 210 GLU cc_start: 0.7892 (tp30) cc_final: 0.7459 (tp30) REVERT: F 59 GLU cc_start: 0.8236 (mt-10) cc_final: 0.8012 (mt-10) REVERT: F 118 LYS cc_start: 0.8062 (tttp) cc_final: 0.7809 (tttm) REVERT: F 120 ILE cc_start: 0.8708 (mm) cc_final: 0.8505 (mm) REVERT: F 173 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8611 (ttm-80) REVERT: F 332 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7762 (tt0) REVERT: F 334 LYS cc_start: 0.7319 (pttt) cc_final: 0.6937 (pttt) REVERT: G 76 ASP cc_start: 0.7923 (p0) cc_final: 0.7694 (p0) REVERT: G 77 MET cc_start: 0.9047 (mmm) cc_final: 0.8834 (mtp) REVERT: G 106 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7650 (mpt180) REVERT: G 107 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7730 (mmtm) REVERT: G 119 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7748 (mtp85) REVERT: G 173 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8321 (ttm110) REVERT: G 210 GLU cc_start: 0.7728 (tp30) cc_final: 0.7149 (tp30) REVERT: G 334 LYS cc_start: 0.7226 (pttt) cc_final: 0.6910 (pttt) REVERT: G 336 TYR cc_start: 0.7772 (p90) cc_final: 0.7038 (p90) REVERT: H 18 MET cc_start: 0.8983 (mmm) cc_final: 0.8773 (mmm) REVERT: H 69 GLN cc_start: 0.8919 (pt0) cc_final: 0.8707 (pt0) REVERT: H 84 MET cc_start: 0.8956 (ttp) cc_final: 0.8721 (ttp) REVERT: H 119 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7745 (mtp85) REVERT: H 263 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7286 (mt-10) REVERT: H 271 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7545 (mm-30) REVERT: H 334 LYS cc_start: 0.7409 (pttt) cc_final: 0.7016 (pttt) REVERT: H 340 ARG cc_start: 0.7369 (ttm170) cc_final: 0.7118 (ttm110) REVERT: H 363 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7222 (mt-10) REVERT: I 17 TYR cc_start: 0.9194 (m-80) cc_final: 0.8910 (m-80) REVERT: I 69 GLN cc_start: 0.8862 (pt0) cc_final: 0.8600 (pt0) REVERT: I 76 ASP cc_start: 0.8055 (p0) cc_final: 0.7838 (p0) REVERT: I 198 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8341 (mmp) REVERT: I 239 ASP cc_start: 0.8319 (t70) cc_final: 0.8088 (t70) REVERT: J 24 ASP cc_start: 0.7958 (p0) cc_final: 0.7727 (p0) REVERT: J 69 GLN cc_start: 0.8933 (pt0) cc_final: 0.8703 (pt0) REVERT: J 119 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7749 (mtp85) REVERT: J 210 GLU cc_start: 0.7887 (tp30) cc_final: 0.7448 (tp30) REVERT: J 263 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7387 (mt-10) REVERT: J 334 LYS cc_start: 0.7134 (pttt) cc_final: 0.6911 (pttt) outliers start: 70 outliers final: 0 residues processed: 655 average time/residue: 0.6999 time to fit residues: 524.9292 Evaluate side-chains 506 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 500 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain I residue 198 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 194 ASN C 253 HIS D 115 HIS D 194 ASN ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN F 194 ASN ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 ASN ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN H 253 HIS I 115 HIS I 194 ASN ** I 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN ** J 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.095421 restraints weight = 30940.442| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.23 r_work: 0.2857 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 28030 Z= 0.172 Angle : 0.580 5.826 37890 Z= 0.307 Chirality : 0.043 0.142 3780 Planarity : 0.005 0.043 5030 Dihedral : 4.948 59.467 3782 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.08 % Allowed : 12.54 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.22 (0.15), residues: 3390 helix: 1.76 (0.15), residues: 1090 sheet: -0.18 (0.17), residues: 890 loop : 0.96 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 340 TYR 0.010 0.001 TYR J 180 PHE 0.021 0.002 PHE I 89 TRP 0.010 0.001 TRP C 32 HIS 0.003 0.001 HIS H 284 Details of bonding type rmsd covalent geometry : bond 0.00397 (28030) covalent geometry : angle 0.57967 (37890) hydrogen bonds : bond 0.04046 ( 1270) hydrogen bonds : angle 4.98278 ( 4212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 560 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8538 (mt-10) REVERT: B 106 ARG cc_start: 0.8250 (mmt90) cc_final: 0.7901 (mmt-90) REVERT: B 107 LYS cc_start: 0.8561 (mtpt) cc_final: 0.7851 (mmtm) REVERT: B 210 GLU cc_start: 0.7972 (tp30) cc_final: 0.7459 (tp30) REVERT: B 332 GLU cc_start: 0.7413 (tt0) cc_final: 0.6985 (tt0) REVERT: B 334 LYS cc_start: 0.7295 (ptmt) cc_final: 0.7033 (pttt) REVERT: C 78 TYR cc_start: 0.8397 (m-80) cc_final: 0.8178 (m-10) REVERT: C 119 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7858 (mtp85) REVERT: C 231 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: C 263 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7214 (mt-10) REVERT: D 22 GLN cc_start: 0.8483 (tt0) cc_final: 0.8258 (tt0) REVERT: D 69 GLN cc_start: 0.8914 (pt0) cc_final: 0.8669 (pt0) REVERT: D 77 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8717 (mmm) REVERT: D 103 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8041 (mtpt) REVERT: D 106 ARG cc_start: 0.8437 (tpt170) cc_final: 0.8215 (mmt-90) REVERT: D 107 LYS cc_start: 0.8680 (mtpt) cc_final: 0.7845 (mmtm) REVERT: D 332 GLU cc_start: 0.8239 (tp30) cc_final: 0.7693 (tt0) REVERT: D 334 LYS cc_start: 0.7191 (pttt) cc_final: 0.6976 (pttt) REVERT: D 337 PHE cc_start: 0.7909 (p90) cc_final: 0.7676 (p90) REVERT: E 69 GLN cc_start: 0.8979 (pt0) cc_final: 0.8727 (pt0) REVERT: E 119 ARG cc_start: 0.8367 (mtp85) cc_final: 0.8013 (mtp85) REVERT: E 210 GLU cc_start: 0.8124 (tp30) cc_final: 0.7733 (tp30) REVERT: E 227 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.7738 (mmm160) REVERT: E 243 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.6989 (tp) REVERT: F 259 LYS cc_start: 0.7520 (tttt) cc_final: 0.7254 (ttmm) REVERT: F 327 ARG cc_start: 0.6827 (tmt-80) cc_final: 0.6598 (tmt-80) REVERT: F 334 LYS cc_start: 0.7275 (pttt) cc_final: 0.6921 (pttt) REVERT: G 106 ARG cc_start: 0.8202 (mmt90) cc_final: 0.7858 (mmt-90) REVERT: G 107 LYS cc_start: 0.8597 (mtpt) cc_final: 0.7885 (mmtm) REVERT: G 210 GLU cc_start: 0.7988 (tp30) cc_final: 0.7481 (tp30) REVERT: H 59 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8738 (mt-10) REVERT: H 78 TYR cc_start: 0.8386 (m-80) cc_final: 0.8157 (m-10) REVERT: H 119 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7872 (mtp85) REVERT: H 231 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8623 (m-30) REVERT: H 263 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7197 (mt-10) REVERT: I 22 GLN cc_start: 0.8484 (tt0) cc_final: 0.8264 (tt0) REVERT: I 69 GLN cc_start: 0.8914 (pt0) cc_final: 0.8669 (pt0) REVERT: I 77 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8716 (mmm) REVERT: I 103 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8045 (mtpt) REVERT: I 106 ARG cc_start: 0.8442 (tpt170) cc_final: 0.8209 (mmt-90) REVERT: I 107 LYS cc_start: 0.8665 (mtpt) cc_final: 0.7836 (mmtm) REVERT: I 239 ASP cc_start: 0.8492 (t70) cc_final: 0.8281 (t70) REVERT: I 337 PHE cc_start: 0.7918 (p90) cc_final: 0.7681 (p90) REVERT: J 69 GLN cc_start: 0.8970 (pt0) cc_final: 0.8719 (pt0) REVERT: J 119 ARG cc_start: 0.8366 (mtp85) cc_final: 0.8004 (mtp85) REVERT: J 210 GLU cc_start: 0.8128 (tp30) cc_final: 0.7737 (tp30) REVERT: J 227 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.7724 (mmm160) REVERT: J 243 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6984 (tp) REVERT: J 259 LYS cc_start: 0.7459 (tttt) cc_final: 0.7068 (tttp) REVERT: J 263 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7186 (mt-10) outliers start: 117 outliers final: 38 residues processed: 633 average time/residue: 0.7416 time to fit residues: 534.7609 Evaluate side-chains 561 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 513 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 237 optimal weight: 0.0000 chunk 276 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 327 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 284 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 69 GLN C 74 ASN D 74 ASN D 115 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN I 74 ASN ** I 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.150733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.093552 restraints weight = 31202.263| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.17 r_work: 0.2818 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 28030 Z= 0.226 Angle : 0.605 6.575 37890 Z= 0.321 Chirality : 0.045 0.153 3780 Planarity : 0.005 0.045 5030 Dihedral : 4.603 22.694 3760 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.87 % Allowed : 15.89 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.13 (0.15), residues: 3390 helix: 1.73 (0.15), residues: 1090 sheet: -0.33 (0.18), residues: 840 loop : 0.87 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 340 TYR 0.012 0.001 TYR F 104 PHE 0.023 0.002 PHE H 256 TRP 0.010 0.002 TRP H 32 HIS 0.009 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00532 (28030) covalent geometry : angle 0.60518 (37890) hydrogen bonds : bond 0.04085 ( 1270) hydrogen bonds : angle 4.87212 ( 4212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 550 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7977 (mtp85) REVERT: A 227 ARG cc_start: 0.9405 (OUTLIER) cc_final: 0.7709 (mmm160) REVERT: A 259 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6601 (ttmp) REVERT: A 327 ARG cc_start: 0.5962 (mmt180) cc_final: 0.5570 (tpt170) REVERT: A 338 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: A 340 ARG cc_start: 0.7502 (ttm110) cc_final: 0.7250 (ttm110) REVERT: B 107 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8207 (mtpp) REVERT: B 119 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: B 210 GLU cc_start: 0.7946 (tp30) cc_final: 0.7395 (tp30) REVERT: B 227 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.7944 (mmm160) REVERT: B 332 GLU cc_start: 0.7360 (tt0) cc_final: 0.6903 (tt0) REVERT: B 334 LYS cc_start: 0.7466 (ptmt) cc_final: 0.7125 (pttt) REVERT: B 338 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7308 (tt0) REVERT: C 59 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8763 (mt-10) REVERT: C 78 TYR cc_start: 0.8448 (m-80) cc_final: 0.8177 (m-10) REVERT: C 119 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7836 (mtp85) REVERT: C 152 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7824 (m-40) REVERT: C 227 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.8256 (mmm160) REVERT: C 259 LYS cc_start: 0.7647 (tttt) cc_final: 0.7278 (ttmm) REVERT: C 263 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7116 (mt-10) REVERT: C 327 ARG cc_start: 0.6065 (mmt180) cc_final: 0.5605 (tpt90) REVERT: C 332 GLU cc_start: 0.8248 (tp30) cc_final: 0.7862 (tt0) REVERT: D 22 GLN cc_start: 0.8526 (tt0) cc_final: 0.8323 (tt0) REVERT: D 69 GLN cc_start: 0.9016 (pt0) cc_final: 0.8771 (pt0) REVERT: D 103 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7833 (mttt) REVERT: D 106 ARG cc_start: 0.8462 (tpt170) cc_final: 0.8202 (mmt90) REVERT: D 107 LYS cc_start: 0.8659 (mtpt) cc_final: 0.7965 (mmtm) REVERT: E 119 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7979 (mtp85) REVERT: E 210 GLU cc_start: 0.8107 (tp30) cc_final: 0.7612 (tp30) REVERT: E 227 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.7735 (mmm160) REVERT: E 243 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.6984 (tp) REVERT: F 106 ARG cc_start: 0.8470 (mmt180) cc_final: 0.8240 (tpp-160) REVERT: F 119 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7959 (mtp85) REVERT: F 227 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.8064 (mmm160) REVERT: F 327 ARG cc_start: 0.7094 (tmt-80) cc_final: 0.6564 (tpt90) REVERT: F 332 GLU cc_start: 0.7610 (tt0) cc_final: 0.6829 (tt0) REVERT: G 106 ARG cc_start: 0.8279 (mmt90) cc_final: 0.8076 (mmt90) REVERT: G 107 LYS cc_start: 0.8480 (mtpt) cc_final: 0.7776 (mmtm) REVERT: G 119 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8133 (ttm-80) REVERT: G 210 GLU cc_start: 0.7955 (tp30) cc_final: 0.7421 (tp30) REVERT: G 227 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.7942 (mmm160) REVERT: G 338 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7245 (tt0) REVERT: H 119 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7916 (mtp85) REVERT: H 122 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: H 152 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7804 (m-40) REVERT: H 227 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.8244 (mmm160) REVERT: H 231 ASP cc_start: 0.9015 (OUTLIER) cc_final: 0.8780 (m-30) REVERT: H 259 LYS cc_start: 0.7615 (tttt) cc_final: 0.7251 (ttmm) REVERT: H 263 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7124 (mt-10) REVERT: H 327 ARG cc_start: 0.6040 (mmt180) cc_final: 0.5590 (tpt90) REVERT: H 332 GLU cc_start: 0.8195 (tp30) cc_final: 0.7780 (tt0) REVERT: I 22 GLN cc_start: 0.8506 (tt0) cc_final: 0.8301 (tt0) REVERT: I 57 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9167 (mm) REVERT: I 69 GLN cc_start: 0.9003 (pt0) cc_final: 0.8760 (pt0) REVERT: I 103 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7843 (mttt) REVERT: I 106 ARG cc_start: 0.8475 (tpt170) cc_final: 0.8213 (mmt90) REVERT: I 107 LYS cc_start: 0.8638 (mtpt) cc_final: 0.7948 (mmtm) REVERT: I 239 ASP cc_start: 0.8481 (t70) cc_final: 0.8220 (t70) REVERT: I 340 ARG cc_start: 0.7632 (ttm110) cc_final: 0.7419 (mpt-90) REVERT: J 119 ARG cc_start: 0.8324 (mtp85) cc_final: 0.7935 (mtp85) REVERT: J 210 GLU cc_start: 0.8113 (tp30) cc_final: 0.7613 (tp30) REVERT: J 227 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.7726 (mmm160) REVERT: J 243 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6983 (tp) REVERT: J 259 LYS cc_start: 0.7409 (tttt) cc_final: 0.7095 (tttp) outliers start: 111 outliers final: 45 residues processed: 612 average time/residue: 0.7315 time to fit residues: 510.8284 Evaluate side-chains 576 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 512 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 22 optimal weight: 0.5980 chunk 229 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 326 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 278 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 242 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 74 ASN C 362 ASN D 115 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN G 362 ASN H 74 ASN H 362 ASN ** I 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.096439 restraints weight = 31075.703| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.16 r_work: 0.2855 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 28030 Z= 0.142 Angle : 0.548 7.453 37890 Z= 0.289 Chirality : 0.042 0.144 3780 Planarity : 0.004 0.043 5030 Dihedral : 4.304 21.066 3760 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.80 % Allowed : 17.21 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.27 (0.15), residues: 3390 helix: 1.92 (0.15), residues: 1090 sheet: -0.33 (0.18), residues: 860 loop : 0.97 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 340 TYR 0.010 0.001 TYR C 104 PHE 0.025 0.002 PHE I 256 TRP 0.008 0.001 TRP D 32 HIS 0.005 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00330 (28030) covalent geometry : angle 0.54838 (37890) hydrogen bonds : bond 0.03555 ( 1270) hydrogen bonds : angle 4.61999 ( 4212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 548 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7883 (mtp85) REVERT: A 227 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.9096 (mmm160) REVERT: A 327 ARG cc_start: 0.5901 (mmt180) cc_final: 0.5640 (tmt-80) REVERT: A 332 GLU cc_start: 0.8094 (tp30) cc_final: 0.7327 (tm-30) REVERT: B 38 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: B 107 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8140 (mtpp) REVERT: B 210 GLU cc_start: 0.7860 (tp30) cc_final: 0.7440 (tp30) REVERT: B 327 ARG cc_start: 0.6223 (mmt180) cc_final: 0.5995 (tmt-80) REVERT: B 332 GLU cc_start: 0.7403 (tt0) cc_final: 0.6925 (tt0) REVERT: B 334 LYS cc_start: 0.7489 (ptmt) cc_final: 0.7104 (pttt) REVERT: B 336 TYR cc_start: 0.8035 (p90) cc_final: 0.7134 (p90) REVERT: C 59 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8710 (mt-10) REVERT: C 78 TYR cc_start: 0.8331 (m-80) cc_final: 0.8108 (m-10) REVERT: C 119 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7868 (mtp85) REVERT: C 152 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7616 (m-40) REVERT: C 259 LYS cc_start: 0.7680 (tttt) cc_final: 0.7319 (ttmm) REVERT: C 263 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7120 (mt-10) REVERT: C 334 LYS cc_start: 0.7396 (pttt) cc_final: 0.7026 (pttp) REVERT: D 22 GLN cc_start: 0.8422 (tt0) cc_final: 0.8175 (tt0) REVERT: D 107 LYS cc_start: 0.8634 (mtpt) cc_final: 0.7947 (mmtm) REVERT: D 110 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8234 (mp0) REVERT: D 198 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8811 (mmp) REVERT: D 332 GLU cc_start: 0.8208 (tp30) cc_final: 0.7604 (tt0) REVERT: E 119 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7926 (mtp85) REVERT: E 210 GLU cc_start: 0.8078 (tp30) cc_final: 0.7607 (tp30) REVERT: E 227 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.7757 (mmm160) REVERT: E 243 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.6988 (tp) REVERT: E 327 ARG cc_start: 0.6399 (mmt180) cc_final: 0.6085 (tpt170) REVERT: F 106 ARG cc_start: 0.8449 (mmt180) cc_final: 0.8103 (tpp-160) REVERT: F 119 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7891 (mtp85) REVERT: F 227 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.9076 (mmm160) REVERT: F 332 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: F 340 ARG cc_start: 0.7489 (ttm110) cc_final: 0.7282 (ttm110) REVERT: G 107 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8156 (mtpp) REVERT: G 119 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.8072 (ttm-80) REVERT: G 210 GLU cc_start: 0.7874 (tp30) cc_final: 0.7317 (tp30) REVERT: G 327 ARG cc_start: 0.6066 (mmt180) cc_final: 0.5794 (tmt-80) REVERT: G 336 TYR cc_start: 0.8028 (p90) cc_final: 0.7083 (p90) REVERT: H 119 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7876 (mtp85) REVERT: H 122 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: H 231 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8618 (m-30) REVERT: H 259 LYS cc_start: 0.7672 (tttt) cc_final: 0.7309 (ttmm) REVERT: H 263 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7123 (mt-10) REVERT: H 327 ARG cc_start: 0.6163 (mmt180) cc_final: 0.5700 (tpt90) REVERT: H 334 LYS cc_start: 0.7391 (pttt) cc_final: 0.7070 (pttp) REVERT: I 22 GLN cc_start: 0.8423 (tt0) cc_final: 0.8183 (tt0) REVERT: I 107 LYS cc_start: 0.8616 (mtpt) cc_final: 0.7925 (mmtm) REVERT: I 110 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8223 (mp0) REVERT: I 198 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8775 (mmp) REVERT: I 239 ASP cc_start: 0.8478 (t70) cc_final: 0.8261 (t70) REVERT: J 104 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.6757 (t80) REVERT: J 106 ARG cc_start: 0.8033 (tpp-160) cc_final: 0.7657 (mmt-90) REVERT: J 119 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7928 (mtp85) REVERT: J 210 GLU cc_start: 0.8084 (tp30) cc_final: 0.7593 (tp30) REVERT: J 227 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.7748 (mmm160) REVERT: J 243 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.6989 (tp) REVERT: J 327 ARG cc_start: 0.6395 (mmt180) cc_final: 0.6064 (tpt170) REVERT: J 334 LYS cc_start: 0.6840 (pttt) cc_final: 0.6276 (ptpp) outliers start: 109 outliers final: 39 residues processed: 607 average time/residue: 0.7098 time to fit residues: 493.6619 Evaluate side-chains 583 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 530 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 104 TYR Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 203 GLU Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 218 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 333 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN B 362 ASN C 69 GLN C 74 ASN C 362 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 152 ASN G 126 ASN G 362 ASN ** I 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.094038 restraints weight = 31137.155| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.18 r_work: 0.2812 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 28030 Z= 0.193 Angle : 0.574 7.854 37890 Z= 0.304 Chirality : 0.043 0.145 3780 Planarity : 0.004 0.044 5030 Dihedral : 4.443 22.224 3760 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.57 % Favored : 96.22 % Rotamer: Outliers : 3.73 % Allowed : 19.02 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.18 (0.15), residues: 3390 helix: 1.84 (0.15), residues: 1090 sheet: -0.39 (0.18), residues: 860 loop : 0.95 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 340 TYR 0.010 0.001 TYR J 78 PHE 0.018 0.002 PHE B 256 TRP 0.009 0.001 TRP C 32 HIS 0.007 0.001 HIS H 253 Details of bonding type rmsd covalent geometry : bond 0.00455 (28030) covalent geometry : angle 0.57408 (37890) hydrogen bonds : bond 0.03788 ( 1270) hydrogen bonds : angle 4.69572 ( 4212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 535 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7883 (mtp85) REVERT: A 134 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: A 227 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.9111 (mmm160) REVERT: A 259 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6685 (ttmp) REVERT: A 327 ARG cc_start: 0.5875 (mmt180) cc_final: 0.5667 (tmt-80) REVERT: B 38 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8562 (pt0) REVERT: B 107 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8190 (mtpp) REVERT: B 210 GLU cc_start: 0.7908 (tp30) cc_final: 0.7354 (tp30) REVERT: B 327 ARG cc_start: 0.6146 (mmt180) cc_final: 0.5909 (tmt-80) REVERT: B 332 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: B 334 LYS cc_start: 0.7443 (ptmt) cc_final: 0.7135 (pttt) REVERT: B 336 TYR cc_start: 0.8022 (p90) cc_final: 0.7177 (p90) REVERT: B 338 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7178 (tt0) REVERT: C 59 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8701 (mt-10) REVERT: C 78 TYR cc_start: 0.8375 (m-80) cc_final: 0.7925 (m-10) REVERT: C 105 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8358 (p0) REVERT: C 106 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7085 (tpp80) REVERT: C 119 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7840 (mtp85) REVERT: C 152 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7803 (m-40) REVERT: C 227 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8295 (mmm160) REVERT: C 259 LYS cc_start: 0.7726 (tttt) cc_final: 0.7344 (ttmm) REVERT: C 263 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7062 (mt-10) REVERT: C 327 ARG cc_start: 0.6217 (mmt180) cc_final: 0.5777 (tpt90) REVERT: C 334 LYS cc_start: 0.7348 (pttt) cc_final: 0.6965 (pttp) REVERT: D 22 GLN cc_start: 0.8500 (tt0) cc_final: 0.8286 (tt0) REVERT: D 106 ARG cc_start: 0.8554 (mpt180) cc_final: 0.8347 (mpt180) REVERT: D 107 LYS cc_start: 0.8549 (mtpt) cc_final: 0.7915 (mmtm) REVERT: D 198 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8828 (mmp) REVERT: D 332 GLU cc_start: 0.8225 (tp30) cc_final: 0.7609 (tt0) REVERT: E 119 ARG cc_start: 0.8324 (mtp85) cc_final: 0.7933 (mtp85) REVERT: E 210 GLU cc_start: 0.8123 (tp30) cc_final: 0.7630 (tp30) REVERT: E 227 ARG cc_start: 0.9405 (OUTLIER) cc_final: 0.7719 (mmm160) REVERT: E 243 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.6990 (tp) REVERT: E 327 ARG cc_start: 0.6430 (mmt180) cc_final: 0.6103 (tpt170) REVERT: F 119 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7883 (mtp85) REVERT: F 227 ARG cc_start: 0.9372 (OUTLIER) cc_final: 0.9105 (mmm160) REVERT: F 327 ARG cc_start: 0.7002 (tmt-80) cc_final: 0.6567 (tpt90) REVERT: F 332 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: G 107 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8212 (mtpp) REVERT: G 119 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8278 (ttm-80) REVERT: G 210 GLU cc_start: 0.7927 (tp30) cc_final: 0.7387 (tp30) REVERT: G 227 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.7997 (mmm160) REVERT: G 327 ARG cc_start: 0.6106 (mmt180) cc_final: 0.5801 (tmt-80) REVERT: G 336 TYR cc_start: 0.8009 (p90) cc_final: 0.7141 (p90) REVERT: H 105 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8405 (p0) REVERT: H 119 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7840 (mtp85) REVERT: H 122 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: H 152 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7812 (m-40) REVERT: H 227 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.8232 (mmm160) REVERT: H 231 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8718 (m-30) REVERT: H 259 LYS cc_start: 0.7702 (tttt) cc_final: 0.7305 (ttmm) REVERT: H 263 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7103 (mt-10) REVERT: H 327 ARG cc_start: 0.6190 (mmt180) cc_final: 0.5765 (tpt90) REVERT: H 334 LYS cc_start: 0.7341 (pttt) cc_final: 0.7014 (pttp) REVERT: I 22 GLN cc_start: 0.8504 (tt0) cc_final: 0.8287 (tt0) REVERT: I 107 LYS cc_start: 0.8555 (mtpt) cc_final: 0.7919 (mmtm) REVERT: I 198 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8818 (mmp) REVERT: I 239 ASP cc_start: 0.8510 (t70) cc_final: 0.8291 (t70) REVERT: J 106 ARG cc_start: 0.8071 (tpp-160) cc_final: 0.7609 (mmt-90) REVERT: J 119 ARG cc_start: 0.8333 (mtp85) cc_final: 0.7939 (mtp85) REVERT: J 210 GLU cc_start: 0.8133 (tp30) cc_final: 0.7638 (tp30) REVERT: J 227 ARG cc_start: 0.9399 (OUTLIER) cc_final: 0.7710 (mmm160) REVERT: J 243 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.6986 (tp) outliers start: 107 outliers final: 56 residues processed: 593 average time/residue: 0.7314 time to fit residues: 494.5038 Evaluate side-chains 595 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 516 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 126 ASN Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 203 GLU Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 308 optimal weight: 4.9990 chunk 178 optimal weight: 0.4980 chunk 272 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 8 HIS C 69 GLN C 74 ASN C 362 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN H 8 HIS H 74 ASN H 362 ASN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.096256 restraints weight = 31143.133| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.15 r_work: 0.2845 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28030 Z= 0.149 Angle : 0.549 8.218 37890 Z= 0.289 Chirality : 0.042 0.139 3780 Planarity : 0.004 0.042 5030 Dihedral : 4.286 21.274 3760 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.51 % Favored : 96.34 % Rotamer: Outliers : 3.73 % Allowed : 19.76 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.33 (0.15), residues: 3390 helix: 1.92 (0.15), residues: 1090 sheet: -0.26 (0.18), residues: 840 loop : 1.01 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 340 TYR 0.010 0.001 TYR F 104 PHE 0.014 0.001 PHE I 204 TRP 0.009 0.001 TRP D 32 HIS 0.004 0.001 HIS H 253 Details of bonding type rmsd covalent geometry : bond 0.00348 (28030) covalent geometry : angle 0.54899 (37890) hydrogen bonds : bond 0.03548 ( 1270) hydrogen bonds : angle 4.58002 ( 4212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 523 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7829 (mtp85) REVERT: A 134 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: A 227 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.9111 (mmm160) REVERT: A 259 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.7071 (ttmm) REVERT: B 38 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8576 (pt0) REVERT: B 107 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8138 (mtpp) REVERT: B 210 GLU cc_start: 0.7842 (tp30) cc_final: 0.7432 (tp30) REVERT: B 336 TYR cc_start: 0.8030 (p90) cc_final: 0.6979 (p90) REVERT: B 338 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6841 (tt0) REVERT: C 59 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8645 (mt-10) REVERT: C 78 TYR cc_start: 0.8386 (m-80) cc_final: 0.7945 (m-10) REVERT: C 105 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8304 (p0) REVERT: C 106 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7097 (tpp80) REVERT: C 119 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7838 (mtp85) REVERT: C 122 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: C 126 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8332 (t0) REVERT: C 259 LYS cc_start: 0.7751 (tttt) cc_final: 0.7387 (ttmm) REVERT: C 263 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7009 (mt-10) REVERT: C 327 ARG cc_start: 0.6233 (mmt180) cc_final: 0.5813 (tpt90) REVERT: C 332 GLU cc_start: 0.8195 (tp30) cc_final: 0.7868 (tt0) REVERT: D 22 GLN cc_start: 0.8426 (tt0) cc_final: 0.8174 (tt0) REVERT: D 106 ARG cc_start: 0.8537 (mpt180) cc_final: 0.8326 (mpt180) REVERT: D 107 LYS cc_start: 0.8566 (mtpt) cc_final: 0.7952 (mmtm) REVERT: D 198 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8806 (mmp) REVERT: D 332 GLU cc_start: 0.8249 (tp30) cc_final: 0.7841 (tp30) REVERT: E 119 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7925 (mtp85) REVERT: E 210 GLU cc_start: 0.8126 (tp30) cc_final: 0.7652 (tp30) REVERT: E 227 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.7702 (mmm160) REVERT: E 243 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.6966 (tp) REVERT: E 327 ARG cc_start: 0.6365 (mmt180) cc_final: 0.6087 (tpt170) REVERT: F 119 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7886 (mtp85) REVERT: F 227 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.9095 (mmm160) REVERT: F 332 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: G 107 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8168 (mtpp) REVERT: G 119 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.8241 (ttm-80) REVERT: G 327 ARG cc_start: 0.6112 (mmt180) cc_final: 0.5823 (tmt-80) REVERT: G 336 TYR cc_start: 0.8019 (p90) cc_final: 0.6961 (p90) REVERT: G 338 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7339 (tt0) REVERT: H 105 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8256 (p0) REVERT: H 119 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7826 (mtp85) REVERT: H 122 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8047 (m-30) REVERT: H 227 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8245 (mmm160) REVERT: H 231 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8669 (m-30) REVERT: H 259 LYS cc_start: 0.7644 (tttt) cc_final: 0.7283 (ttmm) REVERT: H 263 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7018 (mt-10) REVERT: H 327 ARG cc_start: 0.6189 (mmt180) cc_final: 0.5803 (tpt90) REVERT: H 334 LYS cc_start: 0.7315 (pttt) cc_final: 0.6955 (pttp) REVERT: I 22 GLN cc_start: 0.8425 (tt0) cc_final: 0.8176 (tt0) REVERT: I 107 LYS cc_start: 0.8551 (mtpt) cc_final: 0.7914 (mmtm) REVERT: I 239 ASP cc_start: 0.8489 (t70) cc_final: 0.8244 (t70) REVERT: J 104 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6733 (t80) REVERT: J 106 ARG cc_start: 0.8022 (tpp-160) cc_final: 0.7805 (mmt-90) REVERT: J 119 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7920 (mtp85) REVERT: J 210 GLU cc_start: 0.8142 (tp30) cc_final: 0.7663 (tp30) REVERT: J 227 ARG cc_start: 0.9379 (OUTLIER) cc_final: 0.7714 (mmm160) REVERT: J 243 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6954 (tp) outliers start: 107 outliers final: 51 residues processed: 577 average time/residue: 0.7414 time to fit residues: 486.9124 Evaluate side-chains 586 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 515 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 104 TYR Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 203 GLU Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 0 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 276 optimal weight: 0.8980 chunk 316 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 304 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 69 GLN C 74 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN G 126 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 127 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.152191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.095755 restraints weight = 30944.348| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.17 r_work: 0.2858 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28030 Z= 0.165 Angle : 0.563 8.086 37890 Z= 0.297 Chirality : 0.043 0.140 3780 Planarity : 0.004 0.045 5030 Dihedral : 4.326 21.733 3760 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.81 % Favored : 96.02 % Rotamer: Outliers : 3.52 % Allowed : 20.42 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.27 (0.15), residues: 3390 helix: 1.87 (0.15), residues: 1090 sheet: -0.34 (0.18), residues: 840 loop : 1.01 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 340 TYR 0.015 0.001 TYR I 78 PHE 0.016 0.002 PHE I 204 TRP 0.008 0.001 TRP C 32 HIS 0.006 0.001 HIS H 253 Details of bonding type rmsd covalent geometry : bond 0.00389 (28030) covalent geometry : angle 0.56270 (37890) hydrogen bonds : bond 0.03621 ( 1270) hydrogen bonds : angle 4.62623 ( 4212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 525 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8293 (mmt90) cc_final: 0.8012 (tpp-160) REVERT: A 119 ARG cc_start: 0.8193 (mtp85) cc_final: 0.7848 (mtp85) REVERT: A 134 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: A 227 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9109 (mmm160) REVERT: A 259 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.7092 (ttmm) REVERT: B 38 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8621 (pt0) REVERT: B 107 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8177 (mtpp) REVERT: B 210 GLU cc_start: 0.7850 (tp30) cc_final: 0.7438 (tp30) REVERT: B 324 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7208 (ttp80) REVERT: B 327 ARG cc_start: 0.6928 (tmt-80) cc_final: 0.6434 (tmt-80) REVERT: B 332 GLU cc_start: 0.7852 (tp30) cc_final: 0.7290 (tt0) REVERT: B 336 TYR cc_start: 0.8109 (p90) cc_final: 0.7100 (p90) REVERT: B 338 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7326 (tt0) REVERT: C 59 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8682 (mt-10) REVERT: C 78 TYR cc_start: 0.8415 (m-80) cc_final: 0.8039 (m-10) REVERT: C 105 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8416 (p0) REVERT: C 106 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7087 (tpp80) REVERT: C 119 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7847 (mtp85) REVERT: C 122 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: C 126 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 259 LYS cc_start: 0.7677 (tttt) cc_final: 0.7379 (ttmm) REVERT: C 263 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6989 (mt-10) REVERT: C 327 ARG cc_start: 0.6115 (mmt180) cc_final: 0.5786 (tpt90) REVERT: C 332 GLU cc_start: 0.8191 (tp30) cc_final: 0.7873 (tt0) REVERT: D 22 GLN cc_start: 0.8455 (tt0) cc_final: 0.8213 (tt0) REVERT: D 106 ARG cc_start: 0.8586 (mpt180) cc_final: 0.8326 (mmt90) REVERT: D 107 LYS cc_start: 0.8553 (mtpt) cc_final: 0.7920 (mmtm) REVERT: D 198 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8801 (mmp) REVERT: D 332 GLU cc_start: 0.8276 (tp30) cc_final: 0.7533 (tp30) REVERT: D 334 LYS cc_start: 0.7286 (pttt) cc_final: 0.6805 (pttp) REVERT: E 119 ARG cc_start: 0.8295 (mtp85) cc_final: 0.7898 (mtp85) REVERT: E 210 GLU cc_start: 0.8148 (tp30) cc_final: 0.7555 (tp30) REVERT: E 227 ARG cc_start: 0.9399 (OUTLIER) cc_final: 0.7704 (mmm160) REVERT: E 243 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.6961 (tp) REVERT: E 340 ARG cc_start: 0.7506 (ttm110) cc_final: 0.7291 (mpt-90) REVERT: F 106 ARG cc_start: 0.8386 (mmt90) cc_final: 0.8119 (tpp-160) REVERT: F 119 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7882 (mtp85) REVERT: F 227 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.9095 (mmm160) REVERT: F 327 ARG cc_start: 0.6968 (tmt-80) cc_final: 0.6261 (tpt90) REVERT: F 332 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: G 107 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7625 (mmtm) REVERT: G 119 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8239 (ttm-80) REVERT: G 210 GLU cc_start: 0.7852 (tp30) cc_final: 0.7446 (tp30) REVERT: G 327 ARG cc_start: 0.6075 (mmt180) cc_final: 0.5826 (tmt-80) REVERT: G 332 GLU cc_start: 0.7881 (tp30) cc_final: 0.7520 (tt0) REVERT: G 334 LYS cc_start: 0.7468 (pttm) cc_final: 0.7071 (pttt) REVERT: G 336 TYR cc_start: 0.8079 (p90) cc_final: 0.7041 (p90) REVERT: G 338 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7382 (tt0) REVERT: H 105 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8316 (p0) REVERT: H 106 ARG cc_start: 0.8359 (mmt90) cc_final: 0.7937 (tpp-160) REVERT: H 119 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7832 (mtp85) REVERT: H 122 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: H 214 MET cc_start: 0.8930 (tpt) cc_final: 0.8562 (tpp) REVERT: H 227 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8244 (mmm160) REVERT: H 231 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: H 259 LYS cc_start: 0.7633 (tttt) cc_final: 0.7282 (ttmm) REVERT: H 263 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7001 (mt-10) REVERT: H 327 ARG cc_start: 0.6085 (mmt180) cc_final: 0.5781 (tpt90) REVERT: H 334 LYS cc_start: 0.7303 (pttt) cc_final: 0.6981 (pttp) REVERT: I 22 GLN cc_start: 0.8451 (tt0) cc_final: 0.8207 (tt0) REVERT: I 107 LYS cc_start: 0.8526 (mtpt) cc_final: 0.7874 (mmtm) REVERT: I 239 ASP cc_start: 0.8496 (t70) cc_final: 0.8227 (t70) REVERT: J 104 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.6802 (t80) REVERT: J 106 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7798 (mmt-90) REVERT: J 119 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7904 (mtp85) REVERT: J 210 GLU cc_start: 0.8154 (tp30) cc_final: 0.7671 (tp30) REVERT: J 227 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.7687 (mmm160) REVERT: J 243 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6955 (tp) outliers start: 101 outliers final: 51 residues processed: 582 average time/residue: 0.7369 time to fit residues: 488.8370 Evaluate side-chains 585 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 514 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 104 TYR Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 253 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 212 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 151 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN G 126 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 127 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.153394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.096399 restraints weight = 31051.834| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.20 r_work: 0.2873 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28030 Z= 0.132 Angle : 0.540 8.244 37890 Z= 0.284 Chirality : 0.042 0.144 3780 Planarity : 0.004 0.046 5030 Dihedral : 4.171 20.455 3760 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.96 % Allowed : 21.05 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.42 (0.15), residues: 3390 helix: 2.01 (0.15), residues: 1080 sheet: -0.35 (0.18), residues: 840 loop : 1.16 (0.18), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 340 TYR 0.019 0.001 TYR I 78 PHE 0.012 0.001 PHE I 204 TRP 0.009 0.001 TRP I 32 HIS 0.004 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00308 (28030) covalent geometry : angle 0.54048 (37890) hydrogen bonds : bond 0.03426 ( 1270) hydrogen bonds : angle 4.49905 ( 4212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 524 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8520 (ttp) REVERT: A 105 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8273 (p0) REVERT: A 106 ARG cc_start: 0.8290 (mmt90) cc_final: 0.8040 (tpp-160) REVERT: A 119 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7825 (mtp85) REVERT: A 327 ARG cc_start: 0.6177 (mmt180) cc_final: 0.5958 (tmt-80) REVERT: A 332 GLU cc_start: 0.8138 (tp30) cc_final: 0.7321 (tp30) REVERT: A 340 ARG cc_start: 0.7492 (ttm110) cc_final: 0.7240 (mpt-90) REVERT: B 324 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7200 (ttp80) REVERT: B 327 ARG cc_start: 0.6912 (tmt-80) cc_final: 0.6464 (tmt-80) REVERT: B 332 GLU cc_start: 0.7867 (tp30) cc_final: 0.7292 (tt0) REVERT: B 336 TYR cc_start: 0.8087 (p90) cc_final: 0.6957 (p90) REVERT: B 338 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7331 (tt0) REVERT: C 59 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8670 (mt-10) REVERT: C 78 TYR cc_start: 0.8403 (m-80) cc_final: 0.8019 (m-10) REVERT: C 105 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8404 (p0) REVERT: C 106 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7104 (tpp80) REVERT: C 119 ARG cc_start: 0.8180 (mtp85) cc_final: 0.7842 (mtp85) REVERT: C 122 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: C 259 LYS cc_start: 0.7666 (tttt) cc_final: 0.7373 (ttmm) REVERT: C 263 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6906 (mt-10) REVERT: C 327 ARG cc_start: 0.6144 (mmt180) cc_final: 0.5928 (tmt-80) REVERT: C 332 GLU cc_start: 0.8183 (tp30) cc_final: 0.7863 (tt0) REVERT: D 22 GLN cc_start: 0.8401 (tt0) cc_final: 0.8134 (tt0) REVERT: D 106 ARG cc_start: 0.8550 (mpt180) cc_final: 0.8240 (mmt90) REVERT: D 107 LYS cc_start: 0.8564 (mtpt) cc_final: 0.7940 (mmtm) REVERT: D 198 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8764 (mmp) REVERT: D 255 ASN cc_start: 0.8277 (m-40) cc_final: 0.8042 (m110) REVERT: D 332 GLU cc_start: 0.8252 (tp30) cc_final: 0.7526 (tp30) REVERT: D 334 LYS cc_start: 0.7237 (pttt) cc_final: 0.6767 (pttp) REVERT: E 119 ARG cc_start: 0.8279 (mtp85) cc_final: 0.7882 (mtp85) REVERT: E 210 GLU cc_start: 0.8161 (tp30) cc_final: 0.7688 (tp30) REVERT: E 243 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.6949 (tp) REVERT: E 327 ARG cc_start: 0.6342 (mmt180) cc_final: 0.6007 (tmt-80) REVERT: E 340 ARG cc_start: 0.7515 (ttm110) cc_final: 0.7312 (mpt-90) REVERT: F 29 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8511 (ttp) REVERT: F 106 ARG cc_start: 0.8320 (mmt90) cc_final: 0.7994 (tpp-160) REVERT: F 119 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7873 (mtp85) REVERT: F 227 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.9055 (mmm160) REVERT: F 332 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: G 104 TYR cc_start: 0.7351 (t80) cc_final: 0.6982 (t80) REVERT: G 119 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8247 (ttm-80) REVERT: G 327 ARG cc_start: 0.6026 (mmt180) cc_final: 0.5804 (tmt-80) REVERT: G 332 GLU cc_start: 0.7865 (tp30) cc_final: 0.7498 (tt0) REVERT: G 334 LYS cc_start: 0.7428 (pttm) cc_final: 0.6991 (pttt) REVERT: G 336 TYR cc_start: 0.8049 (p90) cc_final: 0.7005 (p90) REVERT: G 338 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7583 (tt0) REVERT: H 105 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8259 (p0) REVERT: H 106 ARG cc_start: 0.8371 (mmt90) cc_final: 0.7967 (tpp-160) REVERT: H 119 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7837 (mtp85) REVERT: H 227 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.9066 (mmm-85) REVERT: H 231 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: H 259 LYS cc_start: 0.7604 (tttt) cc_final: 0.7276 (ttmm) REVERT: H 263 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7036 (mt-10) REVERT: H 334 LYS cc_start: 0.7297 (pttt) cc_final: 0.6952 (pttp) REVERT: I 22 GLN cc_start: 0.8399 (tt0) cc_final: 0.8127 (tt0) REVERT: I 106 ARG cc_start: 0.8371 (mpt180) cc_final: 0.8084 (mpt180) REVERT: I 107 LYS cc_start: 0.8512 (mtpt) cc_final: 0.7842 (mmtm) REVERT: I 239 ASP cc_start: 0.8477 (t70) cc_final: 0.8275 (t70) REVERT: J 119 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7898 (mtp85) REVERT: J 210 GLU cc_start: 0.8139 (tp30) cc_final: 0.7655 (tp30) REVERT: J 243 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.6942 (tp) REVERT: J 327 ARG cc_start: 0.6607 (mmt180) cc_final: 0.6103 (tmt-80) outliers start: 85 outliers final: 42 residues processed: 565 average time/residue: 0.7202 time to fit residues: 465.2073 Evaluate side-chains 562 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 506 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 64 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 252 optimal weight: 0.5980 chunk 291 optimal weight: 0.0870 chunk 297 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 335 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 74 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN G 126 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 127 GLN ** 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 = 0.3753 r_free = 0.3753 target = 0.151565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.094735 restraints weight = 31047.912| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.17 r_work: 0.2845 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 28030 Z= 0.192 Angle : 0.583 8.542 37890 Z= 0.308 Chirality : 0.043 0.150 3780 Planarity : 0.005 0.050 5030 Dihedral : 4.403 21.920 3760 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.10 % Favored : 95.72 % Rotamer: Outliers : 3.10 % Allowed : 21.11 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.26 (0.15), residues: 3390 helix: 1.86 (0.15), residues: 1080 sheet: -0.44 (0.18), residues: 840 loop : 1.08 (0.18), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 340 TYR 0.015 0.001 TYR I 78 PHE 0.018 0.002 PHE I 204 TRP 0.009 0.001 TRP H 32 HIS 0.007 0.001 HIS H 253 Details of bonding type rmsd covalent geometry : bond 0.00453 (28030) covalent geometry : angle 0.58340 (37890) hydrogen bonds : bond 0.03741 ( 1270) hydrogen bonds : angle 4.68014 ( 4212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 530 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8532 (ttp) REVERT: A 105 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8365 (p0) REVERT: A 119 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7850 (mtp85) REVERT: A 134 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: A 259 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7081 (ttmm) REVERT: A 327 ARG cc_start: 0.6038 (mmt180) cc_final: 0.5815 (tmt-80) REVERT: A 332 GLU cc_start: 0.8168 (tp30) cc_final: 0.7328 (tp30) REVERT: B 106 ARG cc_start: 0.8229 (mmt90) cc_final: 0.7873 (mpt180) REVERT: B 210 GLU cc_start: 0.7895 (tp30) cc_final: 0.7479 (tp30) REVERT: B 327 ARG cc_start: 0.6877 (tmt-80) cc_final: 0.6341 (tmt-80) REVERT: B 332 GLU cc_start: 0.7896 (tp30) cc_final: 0.7317 (tt0) REVERT: B 336 TYR cc_start: 0.8137 (p90) cc_final: 0.7101 (p90) REVERT: B 338 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7421 (tt0) REVERT: C 59 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8712 (mt-10) REVERT: C 105 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8406 (p0) REVERT: C 119 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7844 (mtp85) REVERT: C 122 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: C 263 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7029 (mt-10) REVERT: D 22 GLN cc_start: 0.8488 (tt0) cc_final: 0.8264 (tt0) REVERT: D 106 ARG cc_start: 0.8578 (mpt180) cc_final: 0.8334 (mmt90) REVERT: D 107 LYS cc_start: 0.8573 (mtpt) cc_final: 0.7938 (mmtm) REVERT: D 198 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8825 (mmp) REVERT: D 332 GLU cc_start: 0.8270 (tp30) cc_final: 0.7562 (tp30) REVERT: D 334 LYS cc_start: 0.7257 (pttt) cc_final: 0.6779 (pttp) REVERT: E 119 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7847 (mtp85) REVERT: E 210 GLU cc_start: 0.8168 (tp30) cc_final: 0.7614 (tp30) REVERT: E 227 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.7688 (mmm160) REVERT: E 243 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6880 (tp) REVERT: E 327 ARG cc_start: 0.6388 (mmt180) cc_final: 0.6012 (tmt-80) REVERT: F 105 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8324 (p0) REVERT: F 227 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.9079 (mmm160) REVERT: F 327 ARG cc_start: 0.7099 (tmt-80) cc_final: 0.6575 (tpt90) REVERT: F 332 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6696 (tt0) REVERT: G 38 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: G 106 ARG cc_start: 0.8083 (tpp-160) cc_final: 0.7257 (mmt90) REVERT: G 107 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7616 (mmtm) REVERT: G 119 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8225 (ttm-80) REVERT: G 210 GLU cc_start: 0.7857 (tp30) cc_final: 0.7449 (tp30) REVERT: G 327 ARG cc_start: 0.6113 (mmt180) cc_final: 0.5817 (tmt-80) REVERT: G 332 GLU cc_start: 0.7891 (tp30) cc_final: 0.7533 (tt0) REVERT: G 334 LYS cc_start: 0.7416 (pttm) cc_final: 0.6982 (pttt) REVERT: G 336 TYR cc_start: 0.8096 (p90) cc_final: 0.7052 (p90) REVERT: G 338 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7527 (tt0) REVERT: H 87 ASP cc_start: 0.8925 (t0) cc_final: 0.8723 (t0) REVERT: H 105 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8295 (p0) REVERT: H 119 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7823 (mtp85) REVERT: H 227 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8244 (mmm160) REVERT: H 231 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8676 (m-30) REVERT: H 259 LYS cc_start: 0.7580 (tttt) cc_final: 0.7298 (ttmm) REVERT: H 263 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7068 (mt-10) REVERT: H 334 LYS cc_start: 0.7283 (pttt) cc_final: 0.6979 (pttp) REVERT: I 22 GLN cc_start: 0.8481 (tt0) cc_final: 0.8258 (tt0) REVERT: I 106 ARG cc_start: 0.8438 (mpt180) cc_final: 0.8087 (mpt180) REVERT: I 107 LYS cc_start: 0.8524 (mtpt) cc_final: 0.7844 (mmtm) REVERT: I 239 ASP cc_start: 0.8522 (t70) cc_final: 0.8276 (t70) REVERT: J 119 ARG cc_start: 0.8316 (mtp85) cc_final: 0.7907 (mtp85) REVERT: J 210 GLU cc_start: 0.8160 (tp30) cc_final: 0.7667 (tp30) REVERT: J 227 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.7686 (mmm160) REVERT: J 243 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6943 (tp) REVERT: J 327 ARG cc_start: 0.6577 (mmt180) cc_final: 0.6118 (tmt-80) outliers start: 89 outliers final: 52 residues processed: 576 average time/residue: 0.7337 time to fit residues: 482.4095 Evaluate side-chains 578 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 508 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 203 GLU Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 331 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 253 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 329 optimal weight: 1.9990 chunk 287 optimal weight: 0.1980 chunk 89 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 127 GLN ** 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 = 0.3773 r_free = 0.3773 target = 0.153355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.096313 restraints weight = 31050.196| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.18 r_work: 0.2854 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28030 Z= 0.132 Angle : 0.558 10.234 37890 Z= 0.293 Chirality : 0.042 0.141 3780 Planarity : 0.004 0.053 5030 Dihedral : 4.206 20.021 3760 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.68 % Allowed : 22.20 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.35 (0.15), residues: 3390 helix: 1.99 (0.15), residues: 1080 sheet: -0.43 (0.18), residues: 840 loop : 1.11 (0.18), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 340 TYR 0.011 0.001 TYR I 78 PHE 0.012 0.001 PHE I 204 TRP 0.009 0.001 TRP I 32 HIS 0.003 0.001 HIS H 253 Details of bonding type rmsd covalent geometry : bond 0.00307 (28030) covalent geometry : angle 0.55803 (37890) hydrogen bonds : bond 0.03429 ( 1270) hydrogen bonds : angle 4.50221 ( 4212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 509 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6781 (t80) REVERT: A 105 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8215 (p0) REVERT: A 119 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7854 (mtp85) REVERT: A 134 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: A 332 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: A 340 ARG cc_start: 0.7464 (ttm110) cc_final: 0.7214 (mpt-90) REVERT: B 105 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8099 (p0) REVERT: B 327 ARG cc_start: 0.6883 (tmt-80) cc_final: 0.6460 (mpt180) REVERT: B 332 GLU cc_start: 0.7860 (tp30) cc_final: 0.7346 (tt0) REVERT: B 336 TYR cc_start: 0.8124 (p90) cc_final: 0.7054 (p90) REVERT: B 338 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7299 (tt0) REVERT: C 59 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8643 (mt-10) REVERT: C 105 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8325 (p0) REVERT: C 119 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7832 (mtp85) REVERT: C 122 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: C 263 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6947 (mt-10) REVERT: D 22 GLN cc_start: 0.8411 (tt0) cc_final: 0.8145 (tt0) REVERT: D 105 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8294 (p0) REVERT: D 106 ARG cc_start: 0.8520 (mpt180) cc_final: 0.8187 (mmt-90) REVERT: D 107 LYS cc_start: 0.8578 (mtpt) cc_final: 0.7883 (mmtm) REVERT: D 198 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8757 (mmp) REVERT: D 332 GLU cc_start: 0.8236 (tp30) cc_final: 0.7514 (tp30) REVERT: D 334 LYS cc_start: 0.7211 (pttt) cc_final: 0.6737 (pttp) REVERT: E 106 ARG cc_start: 0.8091 (mmt90) cc_final: 0.7823 (mmt180) REVERT: E 107 LYS cc_start: 0.8559 (mtpt) cc_final: 0.7876 (mmtm) REVERT: E 119 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7878 (mtp85) REVERT: E 210 GLU cc_start: 0.8190 (tp30) cc_final: 0.7638 (tp30) REVERT: E 243 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6894 (tp) REVERT: E 327 ARG cc_start: 0.6460 (mmt180) cc_final: 0.6045 (tmt-80) REVERT: E 334 LYS cc_start: 0.6938 (pttt) cc_final: 0.6601 (pttm) REVERT: E 340 ARG cc_start: 0.7543 (ttm110) cc_final: 0.7259 (mpt-90) REVERT: F 105 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8256 (p0) REVERT: F 110 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8131 (mp0) REVERT: F 227 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8969 (mmm160) REVERT: F 332 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6798 (tt0) REVERT: G 105 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7918 (m110) REVERT: G 106 ARG cc_start: 0.7820 (tpp-160) cc_final: 0.7410 (tpp-160) REVERT: G 107 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7597 (mmtm) REVERT: G 119 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8230 (ttm-80) REVERT: G 324 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.7156 (ttp80) REVERT: G 327 ARG cc_start: 0.6035 (mmt180) cc_final: 0.5805 (tmt-80) REVERT: G 332 GLU cc_start: 0.7883 (tp30) cc_final: 0.7530 (tt0) REVERT: G 334 LYS cc_start: 0.7414 (pttm) cc_final: 0.7010 (pttt) REVERT: G 336 TYR cc_start: 0.8060 (p90) cc_final: 0.7003 (p90) REVERT: G 338 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7554 (tt0) REVERT: H 87 ASP cc_start: 0.8913 (t0) cc_final: 0.8711 (t0) REVERT: H 105 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8293 (p0) REVERT: H 119 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7827 (mtp85) REVERT: H 122 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: H 227 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.9056 (mmm-85) REVERT: H 231 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8644 (m-30) REVERT: H 259 LYS cc_start: 0.7558 (tttt) cc_final: 0.7263 (ttmm) REVERT: H 263 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7083 (mt-10) REVERT: H 334 LYS cc_start: 0.7314 (pttt) cc_final: 0.7077 (pttp) REVERT: I 22 GLN cc_start: 0.8411 (tt0) cc_final: 0.8139 (tt0) REVERT: I 106 ARG cc_start: 0.8350 (mpt180) cc_final: 0.8050 (mpt180) REVERT: I 107 LYS cc_start: 0.8511 (mtpt) cc_final: 0.7839 (mmtm) REVERT: J 107 LYS cc_start: 0.8526 (mtpt) cc_final: 0.7856 (mmtm) REVERT: J 119 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7909 (mtp85) REVERT: J 210 GLU cc_start: 0.8174 (tp30) cc_final: 0.7676 (tp30) REVERT: J 243 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6881 (tp) REVERT: J 327 ARG cc_start: 0.6325 (mmt180) cc_final: 0.5980 (tpt90) REVERT: J 332 GLU cc_start: 0.7634 (tp30) cc_final: 0.7031 (tm-30) REVERT: J 334 LYS cc_start: 0.7376 (pttt) cc_final: 0.7125 (pttm) outliers start: 77 outliers final: 44 residues processed: 551 average time/residue: 0.7124 time to fit residues: 449.3741 Evaluate side-chains 558 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 495 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 189 optimal weight: 0.0050 chunk 271 optimal weight: 8.9990 chunk 263 optimal weight: 0.9990 chunk 262 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 293 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN D 8 HIS ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN E 8 HIS ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 HIS ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 HIS ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.097238 restraints weight = 30903.849| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.18 r_work: 0.2851 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28030 Z= 0.134 Angle : 0.563 9.940 37890 Z= 0.297 Chirality : 0.042 0.148 3780 Planarity : 0.004 0.053 5030 Dihedral : 4.212 19.801 3760 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.72 % Allowed : 22.54 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.33 (0.15), residues: 3390 helix: 2.01 (0.15), residues: 1080 sheet: -0.47 (0.18), residues: 840 loop : 1.10 (0.18), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 340 TYR 0.016 0.001 TYR G 78 PHE 0.018 0.001 PHE F 154 TRP 0.008 0.001 TRP I 32 HIS 0.004 0.001 HIS H 253 Details of bonding type rmsd covalent geometry : bond 0.00314 (28030) covalent geometry : angle 0.56308 (37890) hydrogen bonds : bond 0.03424 ( 1270) hydrogen bonds : angle 4.47969 ( 4212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12373.29 seconds wall clock time: 210 minutes 23.31 seconds (12623.31 seconds total)