Starting phenix.real_space_refine on Sun May 25 17:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5n_26356/05_2025/7u5n_26356.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5n_26356/05_2025/7u5n_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_26356/05_2025/7u5n_26356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5n_26356/05_2025/7u5n_26356.map" model { file = "/net/cci-nas-00/data/ceres_data/7u5n_26356/05_2025/7u5n_26356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5n_26356/05_2025/7u5n_26356.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 7.61, per 1000 atoms: 0.28 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: 5.90 Conformation dependent library (CDL) restraints added in 3.3 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: 4.05 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: 10.78 Time building geometry restraints manager: 6.97 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: 0.24 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.930 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: 0.030 Extract box with map and model: 0.890 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 52.040 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.002 TRP E 32 HIS 0.004 0.001 HIS E 284 PHE 0.020 0.002 PHE E 337 TYR 0.009 0.001 TYR C 137 ARG 0.006 0.001 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.16576 ( 1270) hydrogen bonds : angle 7.44548 ( 4212) covalent geometry : bond 0.00552 (28030) covalent geometry : angle 0.92047 (37890) *********************** 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 : 3.254 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: 1.4867 time to fit residues: 1119.0116 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 : 2.966 ------------------------------------------------------------------------------- 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 287 optimal weight: 5.9990 chunk 257 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 266 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 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 194 ASN ** J 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.096536 restraints weight = 30830.158| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.20 r_work: 0.2870 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 28030 Z= 0.168 Angle : 0.578 5.866 37890 Z= 0.305 Chirality : 0.043 0.147 3780 Planarity : 0.005 0.043 5030 Dihedral : 4.939 58.956 3782 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.08 % Allowed : 12.47 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3390 helix: 1.78 (0.15), residues: 1090 sheet: -0.29 (0.17), residues: 910 loop : 1.03 (0.19), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 32 HIS 0.003 0.001 HIS H 284 PHE 0.020 0.002 PHE I 89 TYR 0.010 0.001 TYR J 180 ARG 0.007 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 1270) hydrogen bonds : angle 4.96650 ( 4212) covalent geometry : bond 0.00388 (28030) covalent geometry : angle 0.57776 (37890) *********************** 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 679 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 562 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: B 59 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8538 (mt-10) REVERT: B 106 ARG cc_start: 0.8261 (mmt90) cc_final: 0.7902 (mmt-90) REVERT: B 107 LYS cc_start: 0.8550 (mtpt) cc_final: 0.7837 (mmtm) REVERT: B 210 GLU cc_start: 0.7953 (tp30) cc_final: 0.7434 (tp30) REVERT: B 332 GLU cc_start: 0.7398 (tt0) cc_final: 0.6973 (tt0) REVERT: B 334 LYS cc_start: 0.7272 (ptmt) cc_final: 0.7016 (pttt) REVERT: C 78 TYR cc_start: 0.8372 (m-80) cc_final: 0.8090 (m-10) REVERT: C 119 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7842 (mtp85) REVERT: C 231 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: C 263 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7197 (mt-10) REVERT: D 22 GLN cc_start: 0.8478 (tt0) cc_final: 0.8250 (tt0) REVERT: D 69 GLN cc_start: 0.8929 (pt0) cc_final: 0.8648 (pt0) REVERT: D 103 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8025 (mtpt) REVERT: D 106 ARG cc_start: 0.8438 (tpt170) cc_final: 0.8211 (mmt-90) REVERT: D 107 LYS cc_start: 0.8668 (mtpt) cc_final: 0.7851 (mmtm) REVERT: D 334 LYS cc_start: 0.7161 (pttt) cc_final: 0.6889 (pttt) REVERT: D 337 PHE cc_start: 0.7844 (p90) cc_final: 0.7602 (p90) REVERT: E 69 GLN cc_start: 0.8982 (pt0) cc_final: 0.8725 (pt0) REVERT: E 119 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7993 (mtp85) REVERT: E 210 GLU cc_start: 0.8108 (tp30) cc_final: 0.7711 (tp30) REVERT: E 227 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.7718 (mmm160) REVERT: E 243 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.6990 (tp) REVERT: F 119 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7900 (mtp85) REVERT: F 334 LYS cc_start: 0.7251 (pttt) cc_final: 0.6896 (pttt) REVERT: G 106 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7855 (mmt-90) REVERT: G 107 LYS cc_start: 0.8587 (mtpt) cc_final: 0.7868 (mmtm) REVERT: G 210 GLU cc_start: 0.7973 (tp30) cc_final: 0.7459 (tp30) REVERT: H 59 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8739 (mt-10) REVERT: H 78 TYR cc_start: 0.8368 (m-80) cc_final: 0.8133 (m-10) REVERT: H 119 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7856 (mtp85) REVERT: H 231 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8589 (m-30) REVERT: H 263 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7186 (mt-10) REVERT: I 22 GLN cc_start: 0.8480 (tt0) cc_final: 0.8258 (tt0) REVERT: I 69 GLN cc_start: 0.8912 (pt0) cc_final: 0.8628 (pt0) REVERT: I 103 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8029 (mtpt) REVERT: I 106 ARG cc_start: 0.8441 (tpt170) cc_final: 0.8205 (mmt-90) REVERT: I 107 LYS cc_start: 0.8648 (mtpt) cc_final: 0.7895 (mmtm) REVERT: I 337 PHE cc_start: 0.7855 (p90) cc_final: 0.7612 (p90) REVERT: J 69 GLN cc_start: 0.8971 (pt0) cc_final: 0.8717 (pt0) REVERT: J 119 ARG cc_start: 0.8330 (mtp85) cc_final: 0.7959 (mtp85) REVERT: J 210 GLU cc_start: 0.8109 (tp30) cc_final: 0.7712 (tp30) REVERT: J 227 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.7696 (mmm160) REVERT: J 243 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.6984 (tp) REVERT: J 259 LYS cc_start: 0.7421 (tttt) cc_final: 0.7037 (tttp) REVERT: J 263 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7176 (mt-10) outliers start: 117 outliers final: 38 residues processed: 637 average time/residue: 1.5357 time to fit residues: 1117.6222 Evaluate side-chains 560 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 513 time to evaluate : 2.801 ------------------------------------------------------------------------------- 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 A residue 332 GLU 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 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 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 258 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 69 GLN C 74 ASN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN D 194 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 152 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN G 362 ASN I 74 ASN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.090462 restraints weight = 31172.015| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.17 r_work: 0.2786 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 28030 Z= 0.344 Angle : 0.678 6.386 37890 Z= 0.361 Chirality : 0.049 0.177 3780 Planarity : 0.006 0.053 5030 Dihedral : 4.970 25.346 3760 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.63 % Favored : 96.08 % Rotamer: Outliers : 4.53 % Allowed : 15.19 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 3390 helix: 1.48 (0.15), residues: 1090 sheet: -0.40 (0.17), residues: 910 loop : 0.83 (0.19), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 32 HIS 0.016 0.002 HIS C 253 PHE 0.026 0.003 PHE H 89 TYR 0.017 0.002 TYR D 336 ARG 0.009 0.001 ARG H 340 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 1270) hydrogen bonds : angle 5.10475 ( 4212) covalent geometry : bond 0.00815 (28030) covalent geometry : angle 0.67766 (37890) *********************** 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 649 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 519 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8560 (ttp) REVERT: A 119 ARG cc_start: 0.8314 (mtp85) cc_final: 0.7993 (mtp85) REVERT: A 134 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: A 158 GLN cc_start: 0.8997 (tt0) cc_final: 0.8759 (tt0) REVERT: A 227 ARG cc_start: 0.9436 (OUTLIER) cc_final: 0.7778 (mmm160) REVERT: A 259 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6900 (tttp) REVERT: A 327 ARG cc_start: 0.6020 (mmt180) cc_final: 0.5499 (tpt90) REVERT: A 332 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: A 338 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: B 107 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7729 (mmtm) REVERT: B 119 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8157 (ttm-80) REVERT: B 210 GLU cc_start: 0.7980 (tp30) cc_final: 0.7459 (tp30) REVERT: B 227 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.8204 (mmm160) REVERT: B 263 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7158 (mt-10) REVERT: B 332 GLU cc_start: 0.7341 (tt0) cc_final: 0.6896 (tt0) REVERT: B 334 LYS cc_start: 0.7454 (ptmt) cc_final: 0.7178 (pttt) REVERT: B 336 TYR cc_start: 0.8144 (p90) cc_final: 0.7614 (p90) REVERT: B 338 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7363 (tt0) REVERT: C 119 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7896 (mtp85) REVERT: C 227 ARG cc_start: 0.9413 (OUTLIER) cc_final: 0.7974 (mmm160) REVERT: C 231 ASP cc_start: 0.9128 (OUTLIER) cc_final: 0.8908 (m-30) REVERT: C 263 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7027 (mt-10) REVERT: C 332 GLU cc_start: 0.8231 (tp30) cc_final: 0.7863 (tt0) REVERT: D 57 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9176 (mm) REVERT: D 69 GLN cc_start: 0.9037 (pt0) cc_final: 0.8813 (pt0) REVERT: D 103 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7886 (mttt) REVERT: D 106 ARG cc_start: 0.8474 (tpt170) cc_final: 0.8247 (mmt180) REVERT: D 107 LYS cc_start: 0.8643 (mtpt) cc_final: 0.7933 (mmtm) REVERT: D 332 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7592 (tp30) REVERT: D 334 LYS cc_start: 0.7257 (pttt) cc_final: 0.6859 (ptpp) REVERT: E 119 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7927 (mtp85) REVERT: E 210 GLU cc_start: 0.8093 (tp30) cc_final: 0.7599 (tp30) REVERT: E 227 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.7788 (mmm160) REVERT: E 243 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7013 (tp) REVERT: F 29 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8560 (ttp) REVERT: F 119 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7920 (mtp85) REVERT: F 158 GLN cc_start: 0.9000 (tt0) cc_final: 0.8766 (tt0) REVERT: F 227 ARG cc_start: 0.9414 (OUTLIER) cc_final: 0.7750 (mmm160) REVERT: F 327 ARG cc_start: 0.7027 (tmt-80) cc_final: 0.6398 (ttp80) REVERT: F 332 GLU cc_start: 0.7600 (tt0) cc_final: 0.7052 (tm-30) REVERT: F 338 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: G 106 ARG cc_start: 0.8350 (mmt90) cc_final: 0.7844 (mmt-90) REVERT: G 107 LYS cc_start: 0.8466 (mtpt) cc_final: 0.7764 (mmtm) REVERT: G 119 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8133 (ttm-80) REVERT: G 210 GLU cc_start: 0.7997 (tp30) cc_final: 0.7484 (tp30) REVERT: G 227 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.8264 (mmm160) REVERT: G 239 ASP cc_start: 0.8660 (t70) cc_final: 0.8442 (t70) REVERT: G 263 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7131 (mt-10) REVERT: G 332 GLU cc_start: 0.7394 (tt0) cc_final: 0.7162 (tt0) REVERT: G 336 TYR cc_start: 0.8158 (p90) cc_final: 0.7599 (p90) REVERT: G 338 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7386 (tt0) REVERT: H 57 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9122 (mm) REVERT: H 119 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7853 (mtp85) REVERT: H 122 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: H 227 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.7969 (mmm160) REVERT: H 231 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8902 (m-30) REVERT: H 263 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7002 (mt-10) REVERT: I 57 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9168 (mm) REVERT: I 69 GLN cc_start: 0.9034 (pt0) cc_final: 0.8811 (pt0) REVERT: I 103 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7922 (mttt) REVERT: I 107 LYS cc_start: 0.8635 (mtpt) cc_final: 0.7932 (mmtm) REVERT: J 119 ARG cc_start: 0.8363 (mtp85) cc_final: 0.7974 (mtp85) REVERT: J 210 GLU cc_start: 0.8147 (tp30) cc_final: 0.7664 (tp30) REVERT: J 227 ARG cc_start: 0.9438 (OUTLIER) cc_final: 0.7765 (mmm160) REVERT: J 243 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7024 (tp) REVERT: J 259 LYS cc_start: 0.7442 (tttt) cc_final: 0.7066 (tttp) REVERT: J 263 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7106 (mt-10) outliers start: 130 outliers final: 50 residues processed: 595 average time/residue: 1.5357 time to fit residues: 1044.3041 Evaluate side-chains 576 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 501 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 332 GLU Chi-restraints excluded: chain A residue 338 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 227 ARG Chi-restraints excluded: chain B residue 257 SER 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 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 D residue 57 LEU Chi-restraints excluded: chain D residue 103 LYS 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 212 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 103 LYS 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 29 MET 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 338 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 227 ARG Chi-restraints excluded: chain G residue 257 SER 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 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 277 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 285 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 222 optimal weight: 0.6980 chunk 314 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 315 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 8 HIS C 74 ASN C 253 HIS C 362 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 152 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN G 362 ASN H 8 HIS H 74 ASN H 253 HIS H 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.156795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.098214 restraints weight = 31185.790| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.17 r_work: 0.2908 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2037 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= 0.117 Angle : 0.536 7.684 37890 Z= 0.282 Chirality : 0.042 0.163 3780 Planarity : 0.004 0.040 5030 Dihedral : 4.247 20.580 3760 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 3.31 % Allowed : 18.19 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.15), residues: 3390 helix: 1.93 (0.15), residues: 1090 sheet: -0.18 (0.18), residues: 840 loop : 0.98 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 32 HIS 0.002 0.001 HIS H 253 PHE 0.026 0.001 PHE F 256 TYR 0.010 0.001 TYR A 104 ARG 0.010 0.000 ARG E 340 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1270) hydrogen bonds : angle 4.56188 ( 4212) covalent geometry : bond 0.00261 (28030) covalent geometry : angle 0.53556 (37890) *********************** 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 642 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 547 time to evaluate : 2.809 Fit side-chains revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8213 (mtp85) cc_final: 0.7883 (mtp85) REVERT: B 75 SER cc_start: 0.7748 (p) cc_final: 0.7320 (t) REVERT: B 107 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8142 (mtpp) REVERT: B 210 GLU cc_start: 0.7804 (tp30) cc_final: 0.7333 (tp30) REVERT: B 327 ARG cc_start: 0.6131 (mmt180) cc_final: 0.5905 (tmt-80) REVERT: B 332 GLU cc_start: 0.7390 (tt0) cc_final: 0.6916 (tt0) REVERT: B 334 LYS cc_start: 0.7405 (ptmt) cc_final: 0.7135 (pttt) REVERT: B 336 TYR cc_start: 0.7984 (p90) cc_final: 0.7099 (p90) REVERT: B 340 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7292 (mtp85) REVERT: C 59 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8665 (mt-10) REVERT: C 119 ARG cc_start: 0.8215 (mtp85) cc_final: 0.7898 (mtp85) REVERT: C 152 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7682 (m-40) REVERT: C 231 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: C 259 LYS cc_start: 0.7686 (tttt) cc_final: 0.7356 (ttmm) REVERT: C 263 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7181 (mt-10) REVERT: C 327 ARG cc_start: 0.6486 (mmt180) cc_final: 0.5912 (tpt90) REVERT: C 334 LYS cc_start: 0.7321 (pttt) cc_final: 0.7023 (pttp) REVERT: D 22 GLN cc_start: 0.8368 (tt0) cc_final: 0.8111 (tt0) REVERT: D 107 LYS cc_start: 0.8612 (mtpt) cc_final: 0.7929 (mmtm) REVERT: D 110 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8193 (mp0) REVERT: D 198 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8784 (mmp) REVERT: D 214 MET cc_start: 0.8769 (tpt) cc_final: 0.8487 (tpp) REVERT: D 332 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7683 (tp30) REVERT: D 334 LYS cc_start: 0.7236 (pttt) cc_final: 0.6835 (ptpp) REVERT: E 119 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7881 (mtp85) REVERT: E 210 GLU cc_start: 0.8075 (tp30) cc_final: 0.7583 (tp30) REVERT: E 243 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.6962 (tp) REVERT: E 327 ARG cc_start: 0.6455 (mmt180) cc_final: 0.6018 (tpt170) REVERT: F 106 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7956 (mmt-90) REVERT: F 119 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7832 (mtp85) REVERT: F 332 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: G 107 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8209 (mtpp) REVERT: G 119 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8033 (ttm-80) REVERT: G 210 GLU cc_start: 0.7810 (tp30) cc_final: 0.7206 (tp30) REVERT: G 327 ARG cc_start: 0.6181 (mmt180) cc_final: 0.5910 (tmt-80) REVERT: G 336 TYR cc_start: 0.7961 (p90) cc_final: 0.7020 (p90) REVERT: G 340 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7305 (mtp85) REVERT: H 119 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7889 (mtp85) REVERT: H 122 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: H 152 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7656 (m-40) REVERT: H 231 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8546 (m-30) REVERT: H 259 LYS cc_start: 0.7689 (tttt) cc_final: 0.7334 (ttmm) REVERT: H 263 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7144 (mt-10) REVERT: H 327 ARG cc_start: 0.6469 (mmt180) cc_final: 0.5930 (tpt90) REVERT: H 334 LYS cc_start: 0.7289 (pttt) cc_final: 0.6933 (pttp) REVERT: H 340 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7431 (mpt-90) REVERT: I 22 GLN cc_start: 0.8363 (tt0) cc_final: 0.8105 (tt0) REVERT: I 103 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8009 (mtpt) REVERT: I 107 LYS cc_start: 0.8618 (mtpt) cc_final: 0.7927 (mmtm) REVERT: I 110 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8198 (mp0) REVERT: I 198 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8790 (mmp) REVERT: J 119 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7888 (mtp85) REVERT: J 210 GLU cc_start: 0.8056 (tp30) cc_final: 0.7557 (tp30) REVERT: J 243 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6950 (tp) REVERT: J 259 LYS cc_start: 0.7394 (tttt) cc_final: 0.7021 (tttp) REVERT: J 263 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7029 (mt-10) REVERT: J 327 ARG cc_start: 0.6441 (mmt180) cc_final: 0.6036 (tpt170) outliers start: 95 outliers final: 32 residues processed: 594 average time/residue: 1.4762 time to fit residues: 1006.9942 Evaluate side-chains 571 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 528 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 227 ARG 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 C residue 231 ASP 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 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE 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 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 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 103 LYS 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 152 ASN Chi-restraints excluded: chain J residue 203 GLU 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 55 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 178 optimal weight: 0.1980 chunk 25 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 318 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 chunk 150 optimal weight: 0.0970 chunk 131 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN A 362 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 74 ASN C 362 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 152 ASN F 362 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN G 362 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096220 restraints weight = 30865.657| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.20 r_work: 0.2861 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28030 Z= 0.136 Angle : 0.546 7.799 37890 Z= 0.288 Chirality : 0.042 0.139 3780 Planarity : 0.004 0.045 5030 Dihedral : 4.226 20.376 3760 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.10 % Allowed : 19.83 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 3390 helix: 1.97 (0.15), residues: 1090 sheet: -0.19 (0.18), residues: 840 loop : 1.03 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 32 HIS 0.003 0.001 HIS J 253 PHE 0.018 0.002 PHE F 256 TYR 0.013 0.001 TYR J 104 ARG 0.010 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 1270) hydrogen bonds : angle 4.51600 ( 4212) covalent geometry : bond 0.00317 (28030) covalent geometry : angle 0.54638 (37890) *********************** 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 620 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 531 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7897 (mtp85) REVERT: A 332 GLU cc_start: 0.8091 (tp30) cc_final: 0.7553 (tt0) REVERT: B 38 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: B 75 SER cc_start: 0.7772 (p) cc_final: 0.7393 (t) REVERT: B 107 LYS cc_start: 0.8282 (mtpt) cc_final: 0.8033 (mtpp) REVERT: B 324 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7090 (ttp80) REVERT: B 332 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: B 334 LYS cc_start: 0.7443 (ptmt) cc_final: 0.7123 (pttt) REVERT: B 336 TYR cc_start: 0.7988 (p90) cc_final: 0.7012 (p90) REVERT: B 338 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7296 (tt0) REVERT: C 59 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8691 (mt-10) REVERT: C 105 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8315 (p0) REVERT: C 106 ARG cc_start: 0.8366 (tpp80) cc_final: 0.8061 (tpp-160) REVERT: C 119 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7826 (mtp85) REVERT: C 152 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7690 (m-40) REVERT: C 231 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8564 (m-30) REVERT: C 259 LYS cc_start: 0.7702 (tttt) cc_final: 0.7339 (ttmm) REVERT: C 263 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7069 (mt-10) REVERT: C 327 ARG cc_start: 0.6280 (mmt180) cc_final: 0.5879 (tpt90) REVERT: C 334 LYS cc_start: 0.7323 (pttt) cc_final: 0.6998 (pttp) REVERT: C 340 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7465 (mpt-90) REVERT: D 22 GLN cc_start: 0.8397 (tt0) cc_final: 0.8130 (tt0) REVERT: D 106 ARG cc_start: 0.8524 (mpt180) cc_final: 0.8324 (mpt180) REVERT: D 107 LYS cc_start: 0.8553 (mtpt) cc_final: 0.7938 (mmtm) REVERT: D 198 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8751 (mmp) REVERT: D 332 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7644 (tp30) REVERT: D 334 LYS cc_start: 0.7259 (pttt) cc_final: 0.6832 (ptpp) REVERT: E 107 LYS cc_start: 0.8597 (mtpt) cc_final: 0.7926 (mmtm) REVERT: E 119 ARG cc_start: 0.8300 (mtp85) cc_final: 0.7907 (mtp85) REVERT: E 121 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8115 (mmt) REVERT: E 210 GLU cc_start: 0.8073 (tp30) cc_final: 0.7565 (tp30) REVERT: E 227 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.7766 (mmm160) REVERT: E 243 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.6963 (tp) REVERT: E 327 ARG cc_start: 0.6401 (mmt180) cc_final: 0.6065 (tpt170) REVERT: F 106 ARG cc_start: 0.8175 (tpp-160) cc_final: 0.7894 (mmt-90) REVERT: F 227 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.9104 (mmm160) REVERT: F 332 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: G 107 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8073 (mtpp) REVERT: G 119 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8281 (ttm-80) REVERT: G 336 TYR cc_start: 0.7988 (p90) cc_final: 0.7022 (p90) REVERT: G 338 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7536 (tt0) REVERT: H 105 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8406 (p0) REVERT: H 106 ARG cc_start: 0.8370 (tpp80) cc_final: 0.8059 (tpp-160) REVERT: H 119 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7856 (mtp85) REVERT: H 122 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: H 152 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7658 (m-40) REVERT: H 231 ASP cc_start: 0.8948 (OUTLIER) cc_final: 0.8607 (m-30) REVERT: H 259 LYS cc_start: 0.7573 (tttt) cc_final: 0.7227 (ttmm) REVERT: H 263 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7055 (mt-10) REVERT: H 327 ARG cc_start: 0.6285 (mmt180) cc_final: 0.5850 (tpt90) REVERT: H 334 LYS cc_start: 0.7311 (pttt) cc_final: 0.7053 (pttp) REVERT: I 22 GLN cc_start: 0.8385 (tt0) cc_final: 0.8122 (tt0) REVERT: I 103 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7998 (mtpt) REVERT: I 107 LYS cc_start: 0.8557 (mtpt) cc_final: 0.7909 (mmtm) REVERT: I 110 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8244 (mp0) REVERT: I 198 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8759 (mmp) REVERT: J 119 ARG cc_start: 0.8326 (mtp85) cc_final: 0.7930 (mtp85) REVERT: J 210 GLU cc_start: 0.8045 (tp30) cc_final: 0.7532 (tp30) REVERT: J 227 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.7752 (mmm160) REVERT: J 243 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6959 (tp) REVERT: J 259 LYS cc_start: 0.7480 (tttt) cc_final: 0.7178 (tttp) REVERT: J 263 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7136 (mt-10) outliers start: 89 outliers final: 37 residues processed: 576 average time/residue: 1.5234 time to fit residues: 1007.9322 Evaluate side-chains 566 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 510 time to evaluate : 3.198 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain A residue 212 ILE 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 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 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 231 ASP 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 121 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 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 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 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 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 103 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 92 optimal weight: 4.9990 chunk 313 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 176 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 173 optimal weight: 0.8980 chunk 219 optimal weight: 0.0870 chunk 74 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN F 362 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN H 362 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096481 restraints weight = 31086.652| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.21 r_work: 0.2886 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28030 Z= 0.133 Angle : 0.536 8.139 37890 Z= 0.282 Chirality : 0.042 0.142 3780 Planarity : 0.004 0.043 5030 Dihedral : 4.164 19.556 3760 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.41 % Allowed : 20.45 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 3390 helix: 2.00 (0.15), residues: 1090 sheet: -0.24 (0.18), residues: 840 loop : 1.05 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 32 HIS 0.003 0.001 HIS I 284 PHE 0.017 0.001 PHE F 256 TYR 0.013 0.001 TYR J 104 ARG 0.010 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 1270) hydrogen bonds : angle 4.49253 ( 4212) covalent geometry : bond 0.00311 (28030) covalent geometry : angle 0.53587 (37890) *********************** 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 620 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 522 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8284 (p0) REVERT: A 106 ARG cc_start: 0.8369 (mmt90) cc_final: 0.8106 (tpp-160) REVERT: A 119 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7853 (mtp85) REVERT: A 259 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7078 (ttmm) REVERT: A 327 ARG cc_start: 0.6224 (mmt180) cc_final: 0.5853 (tmt-80) REVERT: A 332 GLU cc_start: 0.8081 (tp30) cc_final: 0.7548 (tt0) REVERT: B 38 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8611 (pt0) REVERT: B 75 SER cc_start: 0.7749 (p) cc_final: 0.7292 (t) REVERT: B 107 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8095 (mtpp) REVERT: B 324 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7112 (ttp80) REVERT: B 332 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: B 336 TYR cc_start: 0.8049 (p90) cc_final: 0.7114 (p90) REVERT: B 338 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7355 (tt0) REVERT: C 59 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8675 (mt-10) REVERT: C 105 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8398 (p0) REVERT: C 106 ARG cc_start: 0.8377 (tpp80) cc_final: 0.7995 (tpp-160) REVERT: C 119 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7829 (mtp85) REVERT: C 152 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7657 (m-40) REVERT: C 227 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.8323 (mmm160) REVERT: C 231 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8642 (m-30) REVERT: C 259 LYS cc_start: 0.7576 (tttt) cc_final: 0.7223 (ttmm) REVERT: C 263 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7046 (mt-10) REVERT: C 327 ARG cc_start: 0.6262 (mmt180) cc_final: 0.5881 (tpt90) REVERT: C 334 LYS cc_start: 0.7311 (pttt) cc_final: 0.6975 (pttp) REVERT: D 22 GLN cc_start: 0.8413 (tt0) cc_final: 0.8138 (tt0) REVERT: D 106 ARG cc_start: 0.8542 (mpt180) cc_final: 0.8243 (mmt90) REVERT: D 107 LYS cc_start: 0.8560 (mtpt) cc_final: 0.7949 (mmtm) REVERT: D 198 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8760 (mmp) REVERT: D 332 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7622 (tp30) REVERT: D 334 LYS cc_start: 0.7250 (pttt) cc_final: 0.6826 (ptpp) REVERT: E 107 LYS cc_start: 0.8591 (mtpt) cc_final: 0.7921 (mmtm) REVERT: E 119 ARG cc_start: 0.8298 (mtp85) cc_final: 0.7902 (mtp85) REVERT: E 121 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8199 (mmt) REVERT: E 210 GLU cc_start: 0.8129 (tp30) cc_final: 0.7633 (tp30) REVERT: E 227 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.7761 (mmm160) REVERT: E 243 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.6948 (tp) REVERT: E 327 ARG cc_start: 0.6357 (mmt180) cc_final: 0.6011 (tmt-80) REVERT: E 340 ARG cc_start: 0.7652 (ttm110) cc_final: 0.7355 (mpt-90) REVERT: F 106 ARG cc_start: 0.8123 (tpp-160) cc_final: 0.7902 (mmt-90) REVERT: F 119 ARG cc_start: 0.8232 (mtp85) cc_final: 0.7965 (mtp85) REVERT: F 134 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: F 227 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.8029 (mmm160) REVERT: F 231 ASP cc_start: 0.9038 (m-30) cc_final: 0.8833 (m-30) REVERT: F 263 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7205 (mt-10) REVERT: F 332 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6771 (tm-30) REVERT: F 340 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7244 (mpt-90) REVERT: G 38 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8604 (pt0) REVERT: G 119 ARG cc_start: 0.8456 (ttm-80) cc_final: 0.8237 (ttm-80) REVERT: G 336 TYR cc_start: 0.8034 (p90) cc_final: 0.7093 (p90) REVERT: G 338 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7565 (tt0) REVERT: H 105 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8464 (p0) REVERT: H 119 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7828 (mtp85) REVERT: H 122 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: H 152 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7641 (m-40) REVERT: H 214 MET cc_start: 0.8850 (tpt) cc_final: 0.8490 (tpp) REVERT: H 227 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8247 (mmm160) REVERT: H 231 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8650 (m-30) REVERT: H 259 LYS cc_start: 0.7563 (tttt) cc_final: 0.7264 (ttmm) REVERT: H 263 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7182 (mt-10) REVERT: H 327 ARG cc_start: 0.6242 (mmt180) cc_final: 0.5859 (tpt90) REVERT: I 22 GLN cc_start: 0.8433 (tt0) cc_final: 0.8182 (tt0) REVERT: I 103 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8032 (mtpt) REVERT: I 107 LYS cc_start: 0.8558 (mtpt) cc_final: 0.7898 (mmtm) REVERT: I 198 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8772 (mmp) REVERT: I 332 GLU cc_start: 0.8123 (tp30) cc_final: 0.7525 (tp30) REVERT: J 119 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7927 (mtp85) REVERT: J 210 GLU cc_start: 0.8087 (tp30) cc_final: 0.7589 (tp30) REVERT: J 227 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.7754 (mmm160) REVERT: J 243 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.6948 (tp) REVERT: J 259 LYS cc_start: 0.7497 (tttt) cc_final: 0.7093 (tttp) REVERT: J 263 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6996 (mt-10) REVERT: J 327 ARG cc_start: 0.6470 (mmt180) cc_final: 0.6093 (tmt-80) outliers start: 98 outliers final: 45 residues processed: 571 average time/residue: 1.5474 time to fit residues: 1013.0092 Evaluate side-chains 569 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 499 time to evaluate : 2.859 ------------------------------------------------------------------------------- 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 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE 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 203 GLU 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 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 C residue 231 ASP 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 121 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 105 ASN Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 134 GLU 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 38 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 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 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 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 198 MET Chi-restraints excluded: chain I residue 212 ILE 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 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 273 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 330 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 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 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 362 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN F 362 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.3759 r_free = 0.3759 target = 0.152196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.095137 restraints weight = 31101.268| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.19 r_work: 0.2847 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28030 Z= 0.165 Angle : 0.563 8.437 37890 Z= 0.297 Chirality : 0.043 0.143 3780 Planarity : 0.004 0.062 5030 Dihedral : 4.304 20.908 3760 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 3.73 % Allowed : 20.87 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.15), residues: 3390 helix: 1.92 (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 TRP 0.008 0.001 TRP C 32 HIS 0.004 0.001 HIS A 253 PHE 0.017 0.002 PHE I 204 TYR 0.015 0.001 TYR B 78 ARG 0.009 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 1270) hydrogen bonds : angle 4.57767 ( 4212) covalent geometry : bond 0.00390 (28030) covalent geometry : angle 0.56321 (37890) *********************** 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 620 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 513 time to evaluate : 3.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8286 (p0) REVERT: A 106 ARG cc_start: 0.8343 (mmt90) cc_final: 0.8092 (tpp-160) REVERT: A 119 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7824 (mtp85) REVERT: A 332 GLU cc_start: 0.8174 (tp30) cc_final: 0.7535 (tt0) REVERT: B 38 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8604 (pt0) REVERT: B 75 SER cc_start: 0.7710 (p) cc_final: 0.7288 (t) REVERT: B 107 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7640 (mmtm) REVERT: B 324 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7165 (ttp80) REVERT: B 332 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: B 336 TYR cc_start: 0.8096 (p90) cc_final: 0.7067 (p90) REVERT: B 338 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7463 (tt0) REVERT: C 59 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8698 (mt-10) REVERT: C 105 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8371 (p0) REVERT: C 106 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8056 (tpp-160) REVERT: C 119 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7828 (mtp85) REVERT: C 227 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8269 (mmm160) REVERT: C 231 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8656 (m-30) REVERT: C 263 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6978 (mt-10) REVERT: C 327 ARG cc_start: 0.6224 (mmt180) cc_final: 0.5993 (tmt-80) REVERT: C 334 LYS cc_start: 0.7317 (pttt) cc_final: 0.6985 (pttp) REVERT: D 22 GLN cc_start: 0.8434 (tt0) cc_final: 0.8197 (tt0) REVERT: D 106 ARG cc_start: 0.8541 (mpt180) cc_final: 0.8234 (mmt90) REVERT: D 107 LYS cc_start: 0.8542 (mtpt) cc_final: 0.7909 (mmtm) REVERT: D 198 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8803 (mmp) REVERT: D 332 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7643 (tp30) REVERT: D 334 LYS cc_start: 0.7268 (pttt) cc_final: 0.6863 (ptpp) REVERT: E 107 LYS cc_start: 0.8601 (mtpt) cc_final: 0.7923 (mmtm) REVERT: E 119 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7915 (mtp85) REVERT: E 121 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8212 (mmt) REVERT: E 210 GLU cc_start: 0.8162 (tp30) cc_final: 0.7607 (tp30) REVERT: E 227 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.7711 (mmm160) REVERT: E 243 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6942 (tp) REVERT: E 327 ARG cc_start: 0.6422 (mmt180) cc_final: 0.6072 (tmt-80) REVERT: E 340 ARG cc_start: 0.7610 (ttm110) cc_final: 0.7368 (mpt-90) REVERT: F 105 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8474 (p0) REVERT: F 134 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: F 227 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8000 (mmm160) REVERT: F 332 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: G 38 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8621 (pt0) REVERT: G 119 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8227 (ttm-80) REVERT: G 332 GLU cc_start: 0.7841 (tp30) cc_final: 0.7036 (tm-30) REVERT: G 336 TYR cc_start: 0.8063 (p90) cc_final: 0.7043 (p90) REVERT: G 338 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7552 (tt0) REVERT: H 87 ASP cc_start: 0.8895 (t0) cc_final: 0.8691 (t0) REVERT: H 105 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8475 (p0) REVERT: H 119 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7812 (mtp85) REVERT: H 122 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: H 214 MET cc_start: 0.8930 (tpt) cc_final: 0.8573 (tpp) REVERT: H 227 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8247 (mmm160) REVERT: H 231 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8664 (m-30) REVERT: H 259 LYS cc_start: 0.7534 (tttt) cc_final: 0.7217 (ttmm) REVERT: H 263 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7103 (mt-10) REVERT: H 334 LYS cc_start: 0.7288 (pttt) cc_final: 0.6982 (pttp) REVERT: I 22 GLN cc_start: 0.8414 (tt0) cc_final: 0.8175 (tt0) REVERT: I 103 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8024 (mtpt) REVERT: I 107 LYS cc_start: 0.8536 (mtpt) cc_final: 0.7878 (mmtm) REVERT: I 110 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8260 (mp0) REVERT: I 198 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8822 (mmp) REVERT: I 332 GLU cc_start: 0.8171 (tp30) cc_final: 0.7526 (tp30) REVERT: J 119 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7902 (mtp85) REVERT: J 210 GLU cc_start: 0.8146 (tp30) cc_final: 0.7648 (tp30) REVERT: J 227 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.7700 (mmm160) REVERT: J 243 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6941 (tp) REVERT: J 259 LYS cc_start: 0.7494 (tttt) cc_final: 0.7293 (tttp) REVERT: J 263 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6904 (pt0) REVERT: J 327 ARG cc_start: 0.6540 (mmt180) cc_final: 0.6117 (tmt-80) outliers start: 107 outliers final: 50 residues processed: 573 average time/residue: 1.5495 time to fit residues: 1017.4262 Evaluate side-chains 574 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 501 time to evaluate : 2.985 ------------------------------------------------------------------------------- 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 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 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 203 GLU 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 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 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 121 MET 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 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 134 GLU 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 38 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER 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 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 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 198 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 269 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 203 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 69 GLN ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN F 362 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.093188 restraints weight = 31018.042| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.17 r_work: 0.2824 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 28030 Z= 0.238 Angle : 0.603 7.996 37890 Z= 0.319 Chirality : 0.045 0.152 3780 Planarity : 0.005 0.062 5030 Dihedral : 4.585 23.060 3760 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.31 % Favored : 95.40 % Rotamer: Outliers : 3.59 % Allowed : 21.36 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.15), residues: 3390 helix: 1.74 (0.15), residues: 1090 sheet: -0.47 (0.18), residues: 840 loop : 0.92 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 32 HIS 0.006 0.001 HIS A 253 PHE 0.020 0.002 PHE I 204 TYR 0.021 0.002 TYR I 78 ARG 0.011 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 1270) hydrogen bonds : angle 4.80252 ( 4212) covalent geometry : bond 0.00565 (28030) covalent geometry : angle 0.60295 (37890) *********************** 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 618 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 515 time to evaluate : 3.043 Fit side-chains revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8339 (p0) REVERT: A 119 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7906 (mtp85) REVERT: A 259 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7116 (ttmm) REVERT: A 327 ARG cc_start: 0.7161 (tmt-80) cc_final: 0.6858 (tpt90) REVERT: A 332 GLU cc_start: 0.8201 (tp30) cc_final: 0.7689 (tt0) REVERT: B 38 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8623 (pt0) REVERT: B 75 SER cc_start: 0.7662 (p) cc_final: 0.7232 (t) REVERT: B 107 LYS cc_start: 0.8467 (mtpt) cc_final: 0.7643 (mmtm) REVERT: B 210 GLU cc_start: 0.7894 (tp30) cc_final: 0.7357 (tp30) REVERT: B 263 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7089 (mt-10) REVERT: B 327 ARG cc_start: 0.6928 (tmt-80) cc_final: 0.6693 (tmt-80) REVERT: B 332 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: B 336 TYR cc_start: 0.8149 (p90) cc_final: 0.7206 (p90) REVERT: B 338 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7346 (tt0) REVERT: C 59 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8728 (mt-10) REVERT: C 105 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8413 (p0) REVERT: C 119 ARG cc_start: 0.8193 (mtp85) cc_final: 0.7844 (mtp85) REVERT: C 227 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.8265 (mmm160) REVERT: C 263 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6941 (mt-10) REVERT: C 327 ARG cc_start: 0.6208 (mmt180) cc_final: 0.5984 (tmt-80) REVERT: C 334 LYS cc_start: 0.7288 (pttt) cc_final: 0.6929 (pttp) REVERT: D 106 ARG cc_start: 0.8578 (mpt180) cc_final: 0.8339 (mmt90) REVERT: D 107 LYS cc_start: 0.8552 (mtpt) cc_final: 0.7914 (mmtm) REVERT: D 126 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8383 (t0) REVERT: D 255 ASN cc_start: 0.8377 (m-40) cc_final: 0.8171 (m110) REVERT: D 332 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7630 (tp30) REVERT: D 334 LYS cc_start: 0.7297 (pttt) cc_final: 0.6894 (ptpp) REVERT: E 107 LYS cc_start: 0.8625 (mtpt) cc_final: 0.7989 (mmtm) REVERT: E 119 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7878 (mtp85) REVERT: E 121 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8219 (mmt) REVERT: E 210 GLU cc_start: 0.8192 (tp30) cc_final: 0.7629 (tp30) REVERT: E 227 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.7727 (mmm160) REVERT: E 243 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.6907 (tp) REVERT: E 327 ARG cc_start: 0.6511 (mmt180) cc_final: 0.6008 (tmt-80) REVERT: F 134 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: F 158 GLN cc_start: 0.8948 (tt0) cc_final: 0.8719 (tt0) REVERT: F 227 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8058 (mmm160) REVERT: F 332 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6890 (tt0) REVERT: G 38 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8596 (pt0) REVERT: G 107 LYS cc_start: 0.8435 (mtpt) cc_final: 0.7610 (mmtm) REVERT: G 119 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: G 210 GLU cc_start: 0.7910 (tp30) cc_final: 0.7367 (tp30) REVERT: G 263 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7066 (mt-10) REVERT: G 336 TYR cc_start: 0.8141 (p90) cc_final: 0.7202 (p90) REVERT: G 338 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7473 (tt0) REVERT: H 105 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8409 (p0) REVERT: H 106 ARG cc_start: 0.8542 (tpt170) cc_final: 0.8284 (tpp-160) REVERT: H 119 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7808 (mtp85) REVERT: H 122 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: H 227 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.8260 (mmm160) REVERT: H 231 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8831 (m-30) REVERT: H 263 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7079 (mt-10) REVERT: H 334 LYS cc_start: 0.7303 (pttt) cc_final: 0.7009 (pttp) REVERT: I 107 LYS cc_start: 0.8533 (mtpt) cc_final: 0.7900 (mmtm) REVERT: I 110 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8195 (mp0) REVERT: I 255 ASN cc_start: 0.8400 (m-40) cc_final: 0.8200 (m110) REVERT: I 332 GLU cc_start: 0.8195 (tp30) cc_final: 0.7642 (tp30) REVERT: J 119 ARG cc_start: 0.8325 (mtp85) cc_final: 0.7911 (mtp85) REVERT: J 210 GLU cc_start: 0.8176 (tp30) cc_final: 0.7611 (tp30) REVERT: J 227 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.7714 (mmm160) REVERT: J 243 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6911 (tp) REVERT: J 259 LYS cc_start: 0.7505 (tttt) cc_final: 0.7226 (tttp) REVERT: J 263 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7239 (mt-10) REVERT: J 327 ARG cc_start: 0.6618 (mmt180) cc_final: 0.6065 (tmt-80) outliers start: 103 outliers final: 50 residues processed: 563 average time/residue: 1.5024 time to fit residues: 968.2711 Evaluate side-chains 559 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 489 time to evaluate : 3.315 ------------------------------------------------------------------------------- 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 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 151 SER Chi-restraints excluded: chain B residue 152 ASN 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 151 SER 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 126 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 3 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 121 MET 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 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 134 GLU 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 38 GLU Chi-restraints excluded: chain G residue 104 TYR 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 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 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 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 267 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 324 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 321 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 255 ASN C 362 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095536 restraints weight = 31144.700| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.20 r_work: 0.2856 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2365 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= 0.146 Angle : 0.568 10.094 37890 Z= 0.298 Chirality : 0.042 0.141 3780 Planarity : 0.004 0.051 5030 Dihedral : 4.330 21.158 3760 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.63 % Favored : 96.14 % Rotamer: Outliers : 3.03 % Allowed : 22.06 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 3390 helix: 1.92 (0.15), residues: 1080 sheet: -0.42 (0.18), residues: 840 loop : 1.07 (0.18), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 32 HIS 0.003 0.001 HIS A 253 PHE 0.014 0.001 PHE C 256 TYR 0.016 0.001 TYR I 78 ARG 0.013 0.001 ARG J 340 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 1270) hydrogen bonds : angle 4.59922 ( 4212) covalent geometry : bond 0.00341 (28030) covalent geometry : angle 0.56806 (37890) *********************** 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 597 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 510 time to evaluate : 3.252 Fit side-chains revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8261 (p0) REVERT: A 119 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7864 (mtp85) REVERT: A 259 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7098 (ttmm) REVERT: A 327 ARG cc_start: 0.7025 (tmt-80) cc_final: 0.6056 (tmt-80) REVERT: A 332 GLU cc_start: 0.8197 (tp30) cc_final: 0.7540 (tt0) REVERT: B 38 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: B 75 SER cc_start: 0.7635 (p) cc_final: 0.7214 (t) REVERT: B 107 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7513 (mmtm) REVERT: B 332 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7019 (tt0) REVERT: B 334 LYS cc_start: 0.7402 (ptmt) cc_final: 0.7172 (pttt) REVERT: B 336 TYR cc_start: 0.8114 (p90) cc_final: 0.7068 (p90) REVERT: B 338 GLU cc_start: 0.7761 (mt-10) cc_final: 0.6809 (tt0) REVERT: C 59 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8661 (mt-10) REVERT: C 105 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8338 (p0) REVERT: C 106 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7972 (tpp-160) REVERT: C 119 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7830 (mtp85) REVERT: C 133 MET cc_start: 0.8837 (mtp) cc_final: 0.8561 (mtp) REVERT: C 263 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6961 (mt-10) REVERT: C 327 ARG cc_start: 0.6219 (mmt180) cc_final: 0.6010 (tmt-80) REVERT: C 334 LYS cc_start: 0.7249 (pttt) cc_final: 0.6901 (pttp) REVERT: D 106 ARG cc_start: 0.8506 (mpt180) cc_final: 0.8245 (mmt90) REVERT: D 107 LYS cc_start: 0.8545 (mtpt) cc_final: 0.7907 (mmtm) REVERT: D 255 ASN cc_start: 0.8352 (m-40) cc_final: 0.8113 (m110) REVERT: D 332 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7634 (tp30) REVERT: D 334 LYS cc_start: 0.7233 (pttt) cc_final: 0.6836 (ptpp) REVERT: E 107 LYS cc_start: 0.8592 (mtpt) cc_final: 0.7966 (mmtm) REVERT: E 119 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7880 (mtp85) REVERT: E 121 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8186 (mmt) REVERT: E 210 GLU cc_start: 0.8186 (tp30) cc_final: 0.7623 (tp30) REVERT: E 227 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.7738 (mmm160) REVERT: E 243 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6959 (tp) REVERT: E 327 ARG cc_start: 0.6261 (mmt180) cc_final: 0.6029 (tmt-80) REVERT: E 340 ARG cc_start: 0.7529 (ttm110) cc_final: 0.7257 (mpt-90) REVERT: F 105 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8337 (p0) REVERT: F 119 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7879 (mtp85) REVERT: F 134 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: F 158 GLN cc_start: 0.8937 (tt0) cc_final: 0.8703 (tt0) REVERT: F 227 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.9069 (mmm160) REVERT: F 332 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: G 38 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8574 (pt0) REVERT: G 107 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7667 (mmtm) REVERT: G 119 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.8227 (ttm-80) REVERT: G 334 LYS cc_start: 0.7129 (pttm) cc_final: 0.6869 (ptpp) REVERT: G 336 TYR cc_start: 0.8092 (p90) cc_final: 0.7049 (p90) REVERT: G 338 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7402 (tt0) REVERT: H 105 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8423 (p0) REVERT: H 119 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7832 (mtp85) REVERT: H 122 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: H 227 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8242 (mmm160) REVERT: H 231 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: H 263 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7083 (mt-10) REVERT: H 327 ARG cc_start: 0.7506 (tmt-80) cc_final: 0.7098 (tmt-80) REVERT: H 334 LYS cc_start: 0.7301 (pttt) cc_final: 0.6916 (pttp) REVERT: I 105 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8115 (p0) REVERT: I 107 LYS cc_start: 0.8503 (mtpt) cc_final: 0.7843 (mmtm) REVERT: I 255 ASN cc_start: 0.8344 (m-40) cc_final: 0.8095 (m110) REVERT: I 332 GLU cc_start: 0.8197 (tp30) cc_final: 0.7656 (tp30) REVERT: J 119 ARG cc_start: 0.8310 (mtp85) cc_final: 0.7907 (mtp85) REVERT: J 210 GLU cc_start: 0.8176 (tp30) cc_final: 0.7603 (tp30) REVERT: J 227 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.7724 (mmm160) REVERT: J 243 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6889 (tp) REVERT: J 263 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6938 (pt0) REVERT: J 327 ARG cc_start: 0.6222 (mmt180) cc_final: 0.5952 (tmt-80) REVERT: J 332 GLU cc_start: 0.7754 (tp30) cc_final: 0.7343 (tt0) REVERT: J 334 LYS cc_start: 0.7349 (pttt) cc_final: 0.6667 (pttm) outliers start: 87 outliers final: 43 residues processed: 555 average time/residue: 1.4852 time to fit residues: 946.5639 Evaluate side-chains 559 residues out of total 2870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 496 time to evaluate : 3.014 ------------------------------------------------------------------------------- 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 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 151 SER Chi-restraints excluded: chain B residue 152 ASN 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 151 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 121 MET 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 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 105 ASN Chi-restraints excluded: chain F residue 134 GLU 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 38 GLU Chi-restraints excluded: chain G residue 104 TYR 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 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1673 > 50: distance: 45 - 70: 18.763 distance: 49 - 76: 24.321 distance: 65 - 70: 15.682 distance: 70 - 71: 15.622 distance: 71 - 72: 16.499 distance: 71 - 74: 11.927 distance: 72 - 73: 26.152 distance: 72 - 76: 11.341 distance: 74 - 75: 23.402 distance: 76 - 77: 6.029 distance: 77 - 78: 17.724 distance: 77 - 80: 14.786 distance: 78 - 79: 17.810 distance: 78 - 84: 24.432 distance: 80 - 81: 17.667 distance: 81 - 82: 18.554 distance: 81 - 83: 19.143 distance: 85 - 86: 15.734 distance: 85 - 88: 10.171 distance: 86 - 87: 31.205 distance: 86 - 92: 10.345 distance: 88 - 89: 9.363 distance: 89 - 90: 5.699 distance: 89 - 91: 22.266 distance: 92 - 93: 17.044 distance: 93 - 94: 19.880 distance: 93 - 96: 8.515 distance: 94 - 95: 12.838 distance: 94 - 100: 10.741 distance: 96 - 97: 15.720 distance: 97 - 98: 6.264 distance: 97 - 99: 10.065 distance: 100 - 101: 7.988 distance: 101 - 102: 16.287 distance: 101 - 104: 5.926 distance: 102 - 103: 14.507 distance: 102 - 109: 30.994 distance: 104 - 105: 6.710 distance: 105 - 106: 8.525 distance: 109 - 110: 19.153 distance: 110 - 111: 18.750 distance: 110 - 113: 11.786 distance: 111 - 112: 13.976 distance: 111 - 116: 8.978 distance: 113 - 114: 16.192 distance: 113 - 115: 14.488 distance: 116 - 117: 17.289 distance: 117 - 118: 26.996 distance: 118 - 119: 21.452 distance: 118 - 120: 29.498 distance: 120 - 121: 4.085 distance: 121 - 122: 19.878 distance: 121 - 124: 16.721 distance: 122 - 123: 10.992 distance: 122 - 128: 20.801 distance: 125 - 126: 3.301 distance: 125 - 127: 7.407 distance: 128 - 129: 42.579 distance: 129 - 130: 3.549 distance: 129 - 132: 15.700 distance: 130 - 131: 40.370 distance: 130 - 137: 9.019 distance: 132 - 133: 14.855 distance: 133 - 134: 19.751 distance: 134 - 135: 3.549 distance: 134 - 136: 13.680 distance: 137 - 138: 40.032 distance: 137 - 143: 40.229 distance: 138 - 139: 5.839 distance: 138 - 141: 40.210 distance: 139 - 140: 8.661 distance: 139 - 144: 27.801 distance: 141 - 142: 40.487 distance: 142 - 143: 6.588